If it’s contra invoicing the best way to do it is to set up a new contra invoicing bank account.
Take a look here:
http://community.quickfile.co.uk/t/contra-invoicing-same-customer-and-supplier-netting-off-receivables-and-payables/345/2?u=parker1090
Your payment in for your invoice would then be tagged to that invoice, and the payment out would be tagged to theirs, leaving nothing in the suspense account