For my part, I will be the initial seed money and overall business operations (finding financing, taxes, general bookkeeping). 

Set it aside to be used exclusively for those "bills".Take the rest, and invest it in flips.Reinvest the profit from those flips into more flips.Once your "seed" money is large enough, continue to flip it...but spend ONLY the profit from those flips on cash flow properties.Repeat....

@Robert Seed, I like the idea of owning a single C class 25 unit complex, as you mentioned- but as @Curt Smith mentioned, getting that commerical $500,000 loan for a first time investor might be tough.

First of two Golden Rules for REI:  Never, under any circumstances, for any reason or rationalization, ever...spend your seed money (your cash). 

My big question is how Do I seed money into the second account to cover the excess mortgage payment or renovations to no commingle the funds ? 

I'm looking to play it straight and use this HELOC for seed money in the new location.

However every giant tree started as a tiny seed.

Is this something I should put some of my seed capital toward on my current flip?

Did selling houses act as your method of raising seed capital?

If you plan on purchasing more houses in the future, strategically set aside seed money for your next purchase, build your cash reserves, pay-off (or down) this house so that it cash-flows and leverage that money (after saving 50% in a contingency fund for vacancies, ect.) into buying another house.An alternate path to consider:http://www.biggerpockets.com/renewsblog/2012/12/12/make-a-million-dollars/Let us know what you decide, and keep us posted!