In the Area Employee Lifecycle (separation ) made for Managers and other HR officers for separation , there should be one similar link in the Employee Area(user). If the Employee is located in far off location and wants to resign he has no better way than to use Email. I would suggest the employee has a SEPARATION link in his Section. He can upload his hand written application with the forms as present in the separation. Once he completes all his formalities in this section the information is immediately shared with the HR manager and Senior officers sharing the software. The manager and other officers (HOD) can write their comments and he maybe allowed to exit with one month notice or as per policy. He would then be given time for exit interview and full and final. The Exit interview forms could be shown once HR manager approves his application for separation and before he comes for Full and final he should fill up form for separation. The date is provided to him from the software for full and final. Once Fand F is done the user account closes in the ERP.
For now, separation is designed to include the process which initiates after resignation of the employee. In your ERPNext account, you can add custom section and fields for the separation process and have email alert configured on the same lines.