How to contra an invoice

I subcontract for one of my suppliers, at the moment when ever I invoice them, they will deduct my invoice from what I owe them, or vice verse, I’m currently putting it down as a refund on my accounts, is there a better way of doing this?

Better open a bank account and call it Contra a/c, tag all payment and receipt to it for contra amounts and actual amounts to main bank a/c