How do I allocate a Journal entry to a Supplier?

Good afternoon,

We have quite a few companies and have a slight issue.  So invoice has arrived for Company 1 and posted in Company 1 but we pay the invoice via company 2.  We have managed to post to the bank account on company 2 and done the appropriate Loan but how do we clear the invoice on company 1 without going through the bank account.  I have tired to do a journal entry but you cannot add it to a specific supplier?  Any help would be greatly appreciated.

Regards

Claire