Yeah keeping track of all the accounts, money and withdrawals can be a bit confusing at times.
Its important to be organised and have a record of how much you have in your bookies, your Betfair account and bank account. And also how much is pending withdrawals.
Ideally you want the majority of your cash to be in your bank or in Betfair. And have enough in whatever bookie you are using.
I like to use a google spreadsheet to keep track of exactly each one of my balances, bank balance and pending withdrawals.
If you want I can share a sheet with you via email.