pay yourself an artist fee, then pay yourself labor.
pay for your overhead- rent, utilities, ongoing costs. figure a rough monthly cost for that stuff, and bill the project.
I guess we all have our methods and criteria, but you said these projects typically have a fixed budget and you have to work backwards from that and figure on 20-30%
With that in mind you can't pay yourself an artist fee or pay yourself labor, or bill the project for anything more than their fixed budget, if you figure 20-30% for the artist fee it leaves only 70-80% of what's left (their maximum budget) to cover everything else.