Hi jpiperni
When you're recording a deposit to your bank account, it will almost always be out of scope except in very specific circumstances where the deposit is lowered by something like a deposit fee or other withholding from your client.
If the transaction is a purchase it may have HST on it.
Generally for purchases you might want to snap the receipts and post them as bills (if being paid later) or expenses (if paid already). Then when the transaction reaches your bank account it'll be a simple match.
Hope this helps!