Hi Janet,
Are you doing a System Check run or Manual Check batches to create your EFT transactions?
There is a company profile option (System Options tab) for consolidating the Bank GL amounts to a single entry for System Check runs (whether or not EFT is used) called 'Post System Checks in Detail', which you would want to disable in order to get a single GL bank entry. The other side of the transactions would still be detailed for each vendor payment. And this option does not affect Manual check batch posting.
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Regards,
Softrak Tech Support