Should I charge clients a setup fee, and can I waive it for one client?

Votel recommends a setup fee when you have to do work up front. A setup fee you can waive also creates urgency, for example: buy my plan and I will waive the $2,500 setup fee.

Set the setup fee on the plan. When you add a plan to a client's account you can override the fee, including setting it to zero for that client, so you do not need a separate plan for every combination.