11)You can create a lookup field on Employee and name it as Manager. You can create a checkbox as well name it as Deactivate. Create a process builder or workflow and define that once the checkbox is checked in the criteria , Action->send an email alert. Use the email template which you would have created.

12)Create a process builder on Project object, check the checkbox when a record is created only, Under immediate action define "Create a record"->choose a rcord type-->Event-->define the required fields under that like status,case origin, Assign to id-Admin User ID and Related to Project record id.
13)Create a process builder on project and define the action under Scheduler, choose the date time field and define 5days before and perform your action under that.
14)CReate a process builder on project , you can define the criteria if End date/time field=Today(-->make it formula) and under immediate action choose update records-->update the status to closed.
15)Again create an approval process and define a process builder on opportunity, if amount >5000, submit approval.
Follow the below link : https://trailhead.salesforce.com/en/projects/build-a-discount-approval-process/steps/create-an-approval-process
Also you dont need to create lot of process builders on Project object , instead you can define the multiple criterias in your case..Hope this would have addressed your requirement.