Customized commission search please help!

We had the commission module until we realized that our commission structure does not allow us to properly use this package.

I worked with NS help to customize a search that would show me all invoices with payments applied in the month I require where the invoice is now "Paid in Full". But I have found numerous issues with this:

1) I need a search based on the invoice status. I want to show all invoices with status changed to "Paid in Full" during a period. I need this because I've found that if payment is received in December but not applied to an invoice (left open on the customer account) no invoice will result in my search for December. If I apply that payment in January to the correct invoice, the "paid in full status" actually back dates to December. Now I have missed the invoice in December, and in January (as my search is limited currently to invoices