The "main" workflow would have to user step: step 1 Employee and step 2 Manager.
You should only have to create one. A lot of the functionality you're looking for are already in LiveCycle.
I would create a two step process: step1 (Employee) and step2 (Manager). When you submit the form to the process, it would go to the first step (Employee). If you have enabled email notification (from adminui), the user associated to the Employee step would receive an new email with the form attached as a PDF.
You could also leverage the Reminders and Deadlines functionality of the user step to receive email notifications when deadlines and/or reminders occurs.
Once the employee is done filling out the form, they can email it back to LiveCycle. You can configure an email endpoint to the built-in Complete Task process. This process will take care of completing the task on step 1 and to send it to step 2 (Manager).
You would need to put the process fields (from Designer) on the form so they contain the task id, server email address, etc.
The only problem is that user might have to login once the Workspace to create their profile to receive the emails. Would that cause a problem?