I Wrote A Check But My Money Is Still There?

Well I have 2 bank accounts, 1 with Navy Federal Credit Union and 1 with Bank of America. Direct deposit with my job is set up with my Navy Fed account but I use my Bank of America account for almost everything. So the other day I needed to send money to my BoA account but didn't have time to set everything up for the online transfers so I just wrote a check to myself from Navy Fed to BoA. Well the next day the check was done processing and the money was in my BoA account. But I checked my Navy Fed account today (4 days later) and the money is still there... Even thought he check has been approved and everything my money is still there 4 days later. Except I'm short $2 so I'm trying to figure out what's going on. I don't know if my money is suddenly going to disappear. I set up transfers today but there's a $3 fee and I don't know if I really even need to pay it...