Hi,
I would suggest you to keep your application related tables separately from the activiti tables.
As far as your leave application process is concerned, create a bpm with 2 user tasks one for the Manager and the other for the employee and your process accepts the employee name, leave from and leave to dates, reason etc.
As far as maintaining users is concerned, you can use your application users only(Maintained in LDAP or in your DB) and not maintain them in activiti. You will have to maintain them in activiti tables only if you are using activiti-explorer.
You can fetch all tasks assigned to user as below
MyProcessEngine.getTaskService().createTaskQuery().taskAssignee(userName).list();
As you must be aware, the above line of code brings you the list of tasks assigned to user with the name you pass. Hence you need not maintain them at multiple places.