how much to charge can be a complicated thing but is something everyone needs to work on a lot.
here a some tips from my personal experience but take it for what it is..just my perspective.
figuring out a formula for how much to charge is different for different types of work.
I have done several short production runs of 50-100 parts at a time where the customer supplied the parts and I just assembled and welded out...and I did pretty well charging a certain amount per tack weld along with a certain amount per linear inch of weld.
the charge per tack weld sort of took care of fit up time for complex parts.
how much per tack and inch depends on things like metal type, whether its tig, mig, or stick...etc.
This is just an FYI but 20 years ago I used a dollar per tack weld and a dollar per inch for stainless TIG and it worked well for me.
at least it gives a starting point.
you might need to adjust the amount up or down for your area and the type of work but the concept works pretty well for production parts.
IF you are the one fronting the money for metal, then you definitely want to mark it up for your risk and trouble.
Another thing to consider is that if you are required to bid a complex job, you need to get paid for the time it took to go over drawings and price materials.
hope this helps.