Once we fix our side up and move in the property should be worth $200k-$250k (it was very undervalued at time of purchase).Why not take a larger loan initial on the purchase of the first duplex and lower your down payment, use the cash you have for the second purchase.  

Current ideas are to view it as a partnership, or an interest-bearing loan from me to him.

The only thing is you would have to do a hard money loan, or find a private money lender that will finance you. 

After living in the primary property in Orlando I figured we could move back to New England and rent that property out which seems like a win-win as far as getting a conventional loan rather an investment loan.

It depends on the loan type and lender.

I have 20k saved and plan to use an FHA 203K loan and house hack to net zero/cash flow minimally on my first investment.

Look into private finance, partnerships, FHA loans, and conventional loans.

It is for sale by owner, but my realtor told me that the owner has an existing wrap loan on it.

Using private money to pay off the deed then looking into equity loans to rehab and purchase other properties.

Assuming you have talked with the seller, I would ask for the requirements for assuming the loan.