We only provide the option of refund at the end of the lease.If there is a deficit in the utilities budget account, we invoice the tenants with the amount due at the first of the next month.  

It's dang near impossible to sort through the noise of the various options of retirement plans and tax consequences and having my funds being immediately available, to take advantage of opportunities as they arise.

We use QuickBooks, to track everything today, all receipts and invoices are notes at the time of purchase which project it is for, then at the end of every week all the receipts and invoices are entered into quickbooks, by "class" each house gets named by its address as a class, thus it is easy to track everything to the respective house, and very easy to get a report weekly for total expenses for each house, as well as to see how much money you made on each house when it closes.

It is a small town and I know him so although there is some concern that I will be left with an incomplete job and out the cash, my bigger concern is being able to prove the expense if audited.He mentioned that he has a contract for me (and him) to sign and I will of course request and invoice but should I also cover myself by creating additional paperwork to be signed? 

But all and all, it is a great software program.In order for anything to show up as Income, you need to type up an Invoice.  

I recently received an invoice from a contractor on some repairs completed.

Dang. 

You're correct with a receipt/invoice and lien waiver.  

I keep a 3 ring binder for my paid invoices (in date order).At year end, place those invoices in a gallon size zip lock bag.

Dang, they're not even usable as a rough estimate?