How do I go about ensuring that at the time of closing, the total cost of fixing plus my fee for the fixing and coordination gets into escrow and I get pay out at the time of close and my brother only gets the remainder from this sale?

Of course this could go up or down, depending on your board of realtors fees and if you decide to purchase leads, etc.  

Here in NY I can't even get one house under contract, so I am not worried about getting 3-5 going.With that said, my biggest hang up was the fact that the deals I found would have been less appealing deals when factoring the loan fees and costs.

If your asking these questions here, find a friend who can help so you don't get fleeced.Drawback is usually the loan is more expensive/higher rate, they may not report to credit agencies (won't improve your credit, but this can keep your documented DTI ratio lower which may be good) and if they do use a servicer, somebody (you, unless you negotiate otherwise) will pay a service fee to have your money processed every month.

I found another agent in my office who wasn't paying for leads so I toss them the ones I don't want and they pay me a referral fee.  

The following expenses must be paid at or prior to closing:   (1) Expenses payable by Seller (Seller's Expenses):      (a) Releases of existing liens, including prepayment penalties and recording fees; release of Seller’s loan liability; tax statements or certificates; preparation of deed; one-half of escrow fee; and other expenses payable by Seller under this contract.      

Now, it really depends on the scope of your project because these fees might be really low and insignificant compared to the total cost of the project.

However, if I don't I will probably just assign it for a small fee and get out of the deal. 

If you had the Dad buy it and then buy it from him you would pay transfer taxes and title fees twice 

They are already getting a development fee.