John,
You should always try to get a formal pricing breakdown in writing before even sending in your material. This should list exactly how the refinery classifies your material, charges applied (treatment charge, settlement charge, melt & assay charge, etc), and payout. The person you are dealing with should be able to work this all out for you on paper and give you an example lot and show final fees and payouts and how they are calculated.
My personal opinion is the more fees it looks like you are being charged the better your payout will be because it's hard to hide things when they are laid out in black and white. Also you want your final invoice to be laid out similarly to your pricing so that you can compare.
A good refinery will offer you multiple options for settlement. Your metal should be able to be sold on the fix or spot of your choosing. Some refineries will even hold the metal for you so that it can be sold at a later time, used towards product, or tranferred to somewhere of your choosing.
Your best bet is to ask lots of questions and get as many answers as you can in writing up front. And definitely whenever you can witness the melt the more at ease you will feel. Any questions about settlement, the refinery should have a procedure in place to deal with that as well.