As far as your EMD from the buyer, that's what keeps them from backing out on you. It should be 20-30% of assignment or 1k,2k,3k, 4k,5k, just depends on your spread. Some ask for all of it upfront, some wait until closing. It has to hurt, or else you have a higher chance of them backing out. The money needs to go hard after their DD period.
Yes, you should have instructions for escrow for Rest of Assignment + EMD to sent to you. Rarely is the EMD given directly to the wholesaler, (Unless you know the buyer or have a relationship) which doesn't allow you to pay for closing fees.
You should speak with a closing company or attorney first, so that way you know the fee structure up front.
This is just general information meant to guide you, not implicit truth. You need to speak with your team (title company, attorney, re agents, brokerage, etc.) first so you know what's suppose to happen and when.
Try to get a mentor or JV a few deals. That will also give you good structure in how to do it, specific to your situation and specific to your market.
EMD-Earnest Money Deposit
DD- Due Diligence