Each time I sync, the Sync Alert comes up and notifies me that all my contacts will be Added, Modified, and Deleted.  If I have 1000 addresses, then it shows 1000 under the Add, Modify, and Delete columns when it should just show the new contacts.

Have I set it up improperly?

I'm transferring from using the CRM package Daylite which has great email integration with Apple Mail. 

I'm evaluating Absolute Automation and MailDrop.  

I like MailDrop better.  Apart from being free, it allows one to be smart about which emails to link versus the inclusive approach of AA.

Am I missing anything?

Although, I wish MailDrop had the ability to link an email to an Account, Opportunity, and Contact all in one click.  It appears to take multipe iterations.

Are there are advantages to AA that I'm missing?