Hi,

This is what I do to avoid the auto apply on credits.

Pay the bill via "Cheque" rather than "pay bill". Select one of the invoices you want to pay on the right hand side - then the rest will show up for selection. Once you have all your invoices selected that you want to pay you can then go back to the right hand side and pick the 1st supplier credit. Again after the 1st one is selected the rest will populate and you can pick the onces you want to use.

Hope this helps.