I have an LLC (S Election) in my state, and I have a friend in another state who has agreed to partner with me, with him bringing the capital for funding flips in my state.

I currently have a single business partner and we're looking to invest in a multi-family and house hack our investment to raise capital and credit for other deals.

@Liwen Gu, it takes time to set up and fund a self directed IRA so you should set the account up before you start lining up investments.

The part I'm having trouble with is funding and how the deal is structured.  

With late cash infusions, work on the house will get delayed.A better option is to secure funding through a Line of Credit, Private Funding, crowd funding, or some other source where there is no red tape to get a $1000 draw. 

I would like to know how most of you fund commercial real estate deals.

I'd like to put $100K down, and fund the rest with a HELOC.

We have no mortgage on the building, as we flipped a large waterfront home for the funds.

If this is a non- prohibited arrangement and thus allowed, how long does it take to set up the self-direct fund and do I use an attorney, my investment company Merrill Lynch or some other professional?

Just like with raising capital from investors, you need credibility with the broker and seller to be taken seriously.