Employees working multiple process levels

I would like to speak to someone regarding employees who work in two or more process levels.  We are an organization with one company, but about 10 different process levels, representing different IDs.  All are independent except one.  We do not use multiple positions, but do assign alt jobs which can be charged at the timeclocks.  Of course, crossing process levels means mutiple W2s.  We do not have a common paymaster.  What I would like to do is see what others are doing and establish what is the best practice based on regulatory requirements as well as ease of account balancing, etc.  Any thoughts/input is much appreciated.