You can add the AP account to the Distribution lines in your import file.  If you are using the Fixed Format, just add the AP account to the Distribution lines.  If you are using the Variable Format, which is based on your Distribution Settings in AP, AP Settings, Invoice Settings, Distribution Settings, you must have the AP account selected as one of the columns to show when entering/importing AP invoices.  It comes after the Expense Account in the import file.  You should use the Variable format if you can - see AP, Help, Import Invoices, Determine text format for importing.

I am using the fixed format.  The problem I have is I am using a different entity to pay the bill so my AP account entity is different from my expense account entity and Sage errors out if they are different.

I see.  Then yes, you will need to make a GL journal entry to redistribute.  Intercompany entries are made in Sage when a cash entry is made.