In this business, as in pretty much every other, a little self-protection goes a long way to helping one sleep at night.
Get a signed subcontract agreement. CART, freelance, do it. Today was the day to renew our CART provision agreement with a local school. It took all of 15 minutes to go over the contract (hey, it was pretty much the same as last semester), but now we all know where we stand. How much the rates are, how we get paid, etc.
If there's a question of how to pay for an after-hours assignment, it's in the contract. Prep work? In the contract. How to handle billing for an agency from out of state? COD in the contract.
It's much easier to have the information UP FRONT than to try to collect later.
Make a New Year's resolution: Get a subcontract agreement for each of the agencies you work with that at least lists out your fees, payment terms, and delivery terms.