We're totally moving in the right direction. Depositing to the UF takes care of the "overdue" invoice issue. My worry though is that we never actually receive the R6.80. 

You are correct, the R6.80 is a bank charge. 

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. 

If I use the UF account, can I then "deposit" the money to bad debts once I'm done? 

I've been sitting with this for days so my head is spinning and I'm over complicating.