I see what you're saying. Since both accounts are showing up in your Chart of Accounts , I recommend entering the transfer as one transaction that affects both accounts. I've found an article which breaks down the process of transfers in QuickBooks. Check it out here when you have a minute. Otherwise, here are the necessary steps which show you how to create a transfer:

1. Select + New.
2. Under Other, select Transfer.
3. From the Transfer Funds From drop down list, select the bank account that the funds are coming out of.
4. From the Transfer Funds To drop down list, select the bank account the funds are being deposited into.
5. In the Transfer Amount field, enter the amount being transferred.
6. Edit the Date.
7. (Optional) Enter a description of the transfer in the Memo field.
8. Select Save and close or Save and new.
9. Select Yes if you double checked the date.

The funds will be transferred as specified. If you have further questions, don't hesitate to reach back.