Kitty:
"Yes" is the answer to both questions. All transactions that affect the bank account either have to originate in the Bank Reconciliation module (such as the ones you described) or pass through from AP, AR or Payroll.

Recent versions of the Bank module will help you with those direct deposits and deductions by allowing you to recognize them in an automated fashion when you are downloading and reconciling your electronic statement. It's more involved than can be addressed in this thread but you can watch the Adagio webinars for full details.