Ron: Thank you for telling me that input fields are passed to the controller. I didn't realize that. That clears up a lot in my head.

We are using javascript on a visualforce page. I think the main reason is because the consultant who helped us set it up wanted it to be easier to maintain. 

... Okay, so I've tried a few different ways of doing this, but the value I type on my visualforce page is still not binding to the value on my Opportunity.

Found this on the sf page developers guide: "The only fields that the <apex:inputField> tag cannot display are those defined as member variables of a custom
controller class written in Apex."

I've tried playing around with a it, but so far no luck. Here's all of the code, just in case. Have highlighted the applicable code in blue.

<apex:page standardController="Opportunity" title="Close Opportunity">

<apex:includeScript value="/soap/ajax/12.0/connection.js"/>
<apex:includeScript value="/soap/ajax/12.0/apex.js"/>

<script type="text/javascript">

/*
** onClickClose
**
** Click handler for "Close Opportunity" button
*/
function onClickClose() {



// Close the opportunity
var status = document.getElementById("{!$Component.f.status}");
status.innerHTML = "Closing opportunity. Please wait...";
document.body.style.cursor = "wait";
setTimeout("closeOpp();", 100);
}


/*
** toggleReason
**
** Toggle UI elements depending on whether the
** Oppportunity is won or lost
*/
function toggleReason() {

// Inspect DOM for UI elements
var wonElement = document.getElementById("{!$Component.f.pb.pbs.si2.isWon}");
var reasonElement = document.getElementById("{!$Component.f.pb.pbs.si3.closeReason}");
var isWon = (wonElement.value == "Yes");


// Remove existing items from reason list
while (reasonElement.options.length > 0) {
reasonElement.remove(0);
}

// Add reasons
if (isWon) {
addReason(reasonElement, "Selected");
addReason(reasonElement, "SOW Signed");
} else {
addReason(reasonElement, "Lost - Competitor");
addReason(reasonElement, "Lost - No Decision");
addReason(reasonElement, "Lost - Insufficient Budget");
addReason(reasonElement, "Lost - Land Survey Selected Instead");
addReason(reasonElement, "Lost - Client Not Selected");
addReason(reasonElement, "Lost - Reason Unknown");
addReason(reasonElement, "Lost - Cancelled");
addReason(reasonElement, "Lost - Change in Scope");
addReason(reasonElement, "Unqualified");
}
reasonElement.selectedIndex = 0;

}


/*
** addReason
**
** Dynamically add items to the reason won/lost
** select list
*/
function addReason(list, reason) {
var opt = document.createElement("option");
opt.text = reason;
opt.value = reason;

if(document.all && !window.opera) {
list.add(opt);
} else {
list.add(opt, null);
}
}


/*
** closeOpp
**
** Closes opportunities and creates
** follow-on projects and opportunities as appropriate
**
** This logic is implemented in Javascript instead of an APEX controller
** extension to avoid the need to maintain and deploy APEX code.
*/
function closeOpp() {

// Set session header
sforce.connection.sessionId = '{!$Api.Session_ID}';

// Get DOM elements
var wonElement = document.getElementById("{!$Component.f.pb.pbs.si2.isWon}");
var reasonElement = document.getElementById("{!$Component.f.pb.pbs.si3.closeReason}");
var won = (wonElement.value == "Yes");
var newDate = document.getElementById("{!$Component.f.pb.pbs.si4.closeDate}");


// Close the current opportunity -- TODO: Flip record type
var oppToClose = new sforce.SObject("Opportunity");
oppToClose.Id = "{!Opportunity.Id}";
oppToClose.StageName = reasonElement.value;

oppToClose.CloseDate = newDate;
//
try {
res = sforce.connection.update([oppToClose]);
} catch (err) {
alert(err);
}

// Retrieve this opp from the database
var thisOpp = retrieveOpp();


// Create recurring Opportunity
if("true" == "{!Opportunity.Recurring__c}") {
createRecurrence(thisOpp);
}

// Create a new project or contract
if (won) {
if ("{!Opportunity.Type}" == "Master Contract / IDIQ") {
var contractId = createContract(thisOpp);
window.location.href="/" + contractId;
} else {
var projectId = createProject(thisOpp);
window.location.href="/" + projectId;
}
} else {
window.location.href="/{!Opportunity.Id}";
}
}


/*
** retrieveOpp
**
** Retrieves the current opportunity as an SObject that can be copied in memory
*/
function retrieveOpp() {
var fields = "";

// Generate list of fields we expect to copy to either an opportunity or project
var dResult = sforce.connection.describeSObject("Opportunity");
for (var i=0; i < dResult.fields.length; i++) {
var f = dResult.fields[i];
fields += (i > 0 ? "," : "") + f.name;
}

// Retrieve the Opportunity
opp = sforce.connection.retrieve(fields, "Opportunity", ["{!Opportunity.Id}"]);
return opp[0];
}


/*
** createRecurrence()
**
** Creates a new recurring opportunity and links it
** to a newly closed opportunity

function createRecurrence(sourceOpp) {
var ret = "";
var res = "";

// Calcuate close date for next occurence
var recurDate = sourceOpp.getDate("CloseDate");
var intervalMonths = sourceOpp.getInt("Recur_Interval_Months__c");
if (intervalMonths) {
recurDate.setMonth(recurDate.getMonth() + intervalMonths);
}

// Initialize new opportunity from closed opportunity
var opp = new sforce.SObject("Opportunity");
opp.AccountId = sourceOpp.AccountId;
opp.Name = sourceOpp.Name;
opp.Amount = sourceOpp.Amount;
opp.StageName = "Needs Analysis"; // TODO -- confirm stage
opp.CloseDate = recurDate;


// TODO -- map additional fields as needed

// Create the Opportunity
try {
res = sforce.connection.create([opp]);
} catch (err) {
alert(err);
}
if (res[0].getBoolean("success")) {
ret = res[0].id;
}

return (ret);
}


/*
** createContract()
** Creates a new contract for a closed opportunity
**
** This logic is implemented in Javascript instead of an APEX controller
** extension to avoid the need to maintain
** and deploy APEX code.
*/
function createContract(sourceOpp) {
var ret = "";
var res = "";

// Initialize contract from Opportunity data
var contract = new sforce.SObject("Contract");
contract.AccountId = sourceOpp.AccountId;
contract.Name = sourceOpp.Name;
contract.Parent_Opportunity__c = sourceOpp.Id;


// Create the contract
try {
res = sforce.connection.create([contract]);
} catch (err) {
alert(err);
}
if (res[0].getBoolean("success")) {
ret = res[0].id;
}

return (ret);
}


/*
** createProject()
**
** Creates a new project and links it to a newly
** closed oppportunity
**
** This logic is implemented in Javascript instead of an APEX controller
** extension to avoid the need for Aero-Metric to maintain
** and deploy APEX code.
*/
function createProject(sourceOpp) {
var ret = "";
var res = "";

// Initialize project from Opportunity data
var project = new sforce.SObject("Summary__c");
project.Name = " - ";
project.projName__c = sourceOpp.Name;
project.projAccount__c = sourceOpp.AccountId;

// TODO -- map additional fields as needed

// Create the project
try {
res = sforce.connection.create([project]);
} catch (err) {
alert(err);
}
if (res[0].getBoolean("success")) {
ret = res[0].id;
}

return (ret);
}


</script>



<apex:sectionHeader title="Close Opportunity" subtitle="{!Opportunity.Name} - Resulting in a {!Opportunity.Type}"/>
<apex:form id="f">
<apex:pageBlock title="Opportunity Win/Loss Information" id="pb">
<apex:pageBlockSection columns="1" title="Why is this Opportunity Closing?" id="pbs">

<apex:outputField value="{!Opportunity.Account.Name}"/>
<apex:outputField value="{!Opportunity.Region_Client_ID__c}"/>
<apex:outputField value="{!Opportunity.Type}"/>

<apex:pageBlockSectionItem id="si1">
<apex:outputLabel value="Current Sales Stage"/>
<apex:outputText value="{!Opportunity.StageName}"/>
</apex:pageBlockSectionItem>


<apex:pageBlockSectionItem id="si2">
<apex:outputLabel value="Did we win this deal?"/>
<apex:selectList id="isWon" size="1" onChange="toggleReason()">
<apex:selectOption itemLabel="Yes" itemValue="Yes"/>
<apex:selectOption itemLabel="No" itemValue="No"/>
</apex:selectList>
</apex:pageBlockSectionItem>

<apex:pageBlockSectionItem id="si3">
<apex:outputLabel value="What was the reason?"/>
<apex:selectList id="closeReason" size="1">
<apex:selectOption itemLabel="Selected" itemValue="Selected"/>
<apex:selectOption itemLabel="SOW Signed" itemValue="SOW Signed"/>
</apex:selectList>
</apex:pageBlockSectionItem>

<apex:pageBlockSection >
<apex:outputLabel value="Close Date"/>
<apex:inputField id="closeDate" value="{!Opportunity.CloseDate}"/>
</apex:pageBlockSection>



</apex:pageBlockSection>
</apex:pageBlock>

<input class="btn" type="button" title="Close Opportunity" name="close" value=" Close Opportunity " onClick="onClickClose()"/>
<apex:commandButton action="{!cancel}" value="Cancel" id="cancelButton"/>
<apex:outputText value="" id="status"/>

</apex:form>

</apex:page>