Not to mention I didn't pay at time of order, that's how legit account's work, net 30 too net 90. meaning I get an invoice monthly or quarterly that we than remit payment to. 

Side note, she was able to get into this property for just under $13k and we we're able to negotiate the seller putting in a new AC unit as well as paying a $7000 invoice to a contractor to replace the roof.Moreover, if your credit is solid, I'd opt toward a 5% down conventional loan if you're leaning toward the 3.5% down FHA route.

Instead he/she claims that his/her invoice is sufficient.

This typically looks like 2 weeks of work before sending our first invoice with proof of work that was completed.

While a software might not be necessary at this stage with your rentals, you should probably at least upload all your files (leases, invoices, etc.) to Google Drive at a minimum.

How do I invoice my company to recoop the interest and the payments on the principal? 

You could try and itemize the invoice and DIY the cost seg for the bathroom reno.

I would have the plumber create an invoice and send it to her.

How would I do that - send them a formal invoice or request, or can it be less formal like a simple email? 

If there is not invoice, then that should be the end of it.