Hi Jessica,Congrats on purchasing a home and best of luck on the repairs.Ideally, the costs that he has been occurring can be marked as contributions to his capital account and expensed my the LLC or expensed on his personal taxes as a supplemental business expense.Sounds like the record keeping is going to be messy and I can't tell you the best way to report this without getting deeper into the books/records to figure out whats going on.If you're open to remote accountants we can hop an a phone call so I can get an understanding of your situation and if we'd be a good fit.

We want to use our money to make our lives easier and be able to supplement our income so that we don't have to work on jobs we don't like. 

I am looking for a small multi-family ideally but single family would work too, and for my first deal(s) cash-flow is my main goal, as I want to supplement my income (I know I am asking for a lot with that in today's market).

We are hoping to have a decent portfolio built in the next 5-10 years to help supplement our income and hopefully give us some more free time from our 9-5 for when we decide to start a family. 

We have even gotten to the point where our townhome development is offering new buyers a payment supplement program for 24 months just to drive sales.

Could they find a third to supplement the rent?

You used the phrase "replace our income" vs. supplement, so I am taking this to mean you intend to quit your W-2 jobs and go full time real estate once you get to the end of your plan.I am sure you realize that $10,000 / month from rents isn't like $10,000 pay check. 

I was prepared for the new property tax amount as a percentage of the sale price but I wasn't prepared for the supplemental tax invoice which is separate from escrow and I still don't fully understand how it is calculated. 

Figure out a way to supplement your real estate business until you can start earning more.

(b)Or ask your plan checker for a supplemental to change the scope of work... this way you do not go back to the beginning of the process, and you keep the plan checker that is already familiar with your situation.