Thank you. I understand what you've done here. 

Instead of matching R1891.27, I will match R1898.07 and "deduct" the R6.80 using the resolve button. Can't believe I didn't think of that. 

If i continue to use this as an example:

"So lets say I invoice a client for R1898.07. We run the debit order for the R1898.07. However, we only receive R1891.27. I use the "match" function to record this payment which then obviously leaves me with R6.80 unaccounted for. "

Unfortunately though, I do not have the time to undo 1000's of transactions to redo them. Is there no other way to sort this out?

I will use this method for future transactions though. 

Thanks