Invoices go into the CC account the same as they would in the AP account and are attributed to the vendor who issues them.  

I keep track of expenses as they come in (I have a notebook) for each rental and file the invoices/bills/etc as soon as they come in and are paid. 

Congrats on finishing up the rehab, as others have mentioned, make sure to document your work.Keep the invoices handy.

I invoiced an extra 25 dollars for part of the cleaning that I needed done extra and it was disregarded.

So I understand, you are charging the tenants a $145 invoice because the plumber was unable to find anything wrong with the garbage disposal.

How  do i know the contractor not cut corner, the seller refuse to disclose the scope of work done, and the contractor said he won't reveal it without seller permission, so they are basically say we won't give you any information beside invoice, other figure it out yourself with your own money, we don't' have obligation.

I had a guest cancel as well and my cleaner refunded the fee from their invoice no problem.

Paying bills, invoicing, etc count, but it will be hard to say it took 750 hours! 

Enter a maintenance request, assign a vendor, and attach a fake invoice.

If you only have one LLC and don’t need entity tracking, you could get a lower subscription and categorize your properties as ‘customers’, then units and tenants would be sub-customers.Simple Start would allow you to invoice your tenants (if desired through QBO) and produce basic reports.