I wouldn't do a Journal Entry.

Set up "Other Liability Account" (Loan to Company B). Then write a check to the vendor from Company A using the (Loan to Company B) Account..

Next write a check to Company A from Company B, under the expense tab enter "Accounts Payable", under customer:job in the check enter in the Vendor. This creates a credit on the vendor's  account.

Go to pay bills, click on the vendor's bill and click on apply credits.

Deposit the check in record deposits from Compay B into Company A. use (Loan to Company B) account.

This should do it.