What part of the mortgage process do I negotiate?

You negotiate everything at once.  You are entering into a contract.  You don't write/sign the contract and THEN negotiate.  BTW, what are you negotiating?

Later in the process?  No. Any negotiating you think you can get away with needs to be done - and the terms you think you are getting, in writing - BEFORE you sign the loan application and pay the upfront fees.  Once you do that, there is no negotiating.

Everything is negotiable.  Compare the two estimates and notice the differences in lender charges (not prepaid estimates).  Of course the interest rate too.  Talk to your realtor as they can advise you on which charges are negotiable and how to approach the mortgage broker about it.  FYI anyone who tells you that you can't negotiate the loan terms is either ignorant or lacks a backbone, likely a little of both.

There usually is not any negotiation.  You pick the best deal.

You don't... you applied to find out what the cost of getting a mortgage loan from them is, you except or not, its simple........

"am I supposed to try and get fees waived or am I supposed to wait until later in the process when I get my final look"  

Once you apply for the loan you've already accepted the terms.   You definitely don't accept the price quote, agree to buy the product and then later argue about the price.   WTH?

Shop around and pick the loan you think is best.   That's it.

You don't negotiate the mortgage process.

You are told that your interest rate is X, the APR is Y, Origination fees are Z, appraisal fees are Q and any other fees that the lender has like an application fee.

You compare those to different lenders and select the one that is right for you.

Just like if you are buying a new TV.  You don't negotiation.  You find the one that has the best lowest cost for you. 

Having the lowest interest rate does not mean it's automatically going to be the lowest cost.