why don't all my deposits show up on my profit and loss report
"Deposits" will never show on P&L (Income Statement), which is Revenue and Expenses only.
Deposits are debit entries to Cash account, which is on the Balance sheet.
Need to find where the credit entries are going. Look at the transaction see both sides of entry.
Normally, you would generate customer invoices which go to Revenue account on P&L and AR account on Balance sheet and then would post Customer receipts when you receive payment.