Is it best to try and first negotiate with them and see what their goals are?  

I have negotiated a "sub to" deal where I will be paying the owner $3,000 and getting the deed subject to an existing mortgage. 

I'm comfortable with negotiating, inspections & talking with contractors etc...What I cant seem to figure out is: the next step after a offer has been made on an off market deal and excepted by the homeowner.Is there any good books that go over this? 

Negotiate. 

@Curtis Mitchell closing cost are going to depend on the lender and can sometimes be negotiated to have the seller include closing costs in the purchase price to decrease the total amount of cash you outlay.In regards to PMI, that is usually an additional percentage of the loan that is added to the payment each month.

How did you find this deal and how did you negotiate it?

Also, how can I effectively negotiate closing cost terms?

If you're licensed or unlicensed, will determine how you negotiate buyer side commissions.

You would in a sense be working for him, so a fee equal to a salary you can live on sounds about right (at least to negotiate).

However, you're not really in the deal at all and it's totally up to the end buyer to negotiate, get the deal to closing, etc.