Since I don't have access to a version 10 installation here, I'll give you the version 9 process.
The window that you are looking for is found under Transactions > Financial > Bank Transactions. The type of transaction will be either a decrease or increase depending on the type of EFT transaction that you are working with. Since your G/L is already correct because of the previous journal entry, you only want to get the same transaction amount into the Bank Rec module so that you will have something to reconcile to your bank statement. When you enter the amount of your EFT transaction into the Bank Transaction Entry screen, the system will automatically populate the corresponding G/L account, for the bank, and amount into the grid in the bottom half of the screen. I always have my clients make the offsetting entry to the bank account as well. This has no effect on the G/L balance because it nets to zero as both the debit and credit go to the same place. The key is to use the same account for both the debit and credit halves of the entry so as not to throw something out of balance. You now have a Bank Rec transaction that has not affected your G/L and you can proceed with your reconciliation process.
From this point onward, you should use this same Transaction Entry screen to make these EFT entries to the bank by replicating what you would have put in the journal entry. As with an A/R or A/P entry, you need to affect both the sub-ledger (the Bank Rec module) as well as the G/L and the only way to keep it all in sync is to initiate the entries from the sub-ledger. If the journal entries were not originating in the G/L, this process may have to be adjusted somewhat to achieve the desired results.
I hope that this helps. If anything is still unclear, post back with your further questions.
Lyle