Why are my deposits showing up as payments in separate bank accounts when all of the money is going into the main account and then being transferred to the sub account?

Thanks for posting here in the Community, @treasurer-bethel. Let me provide information on why deposits are showing as payments in QuickBooks Online (QBO).

QuickBooks acts as the receiver of your financial institution's information. By this, whatever data is reflected to QuickBooks will depend on what is sent by them. I'd suggest connecting only the sub-account and not the primary account. You can check for additional information when connecting the accounts in QuickBooks Online. 

In the meantime, just to make sure why these transactions are showing as deposits in the main account and payments in the sub-account, it's best to contact your financial institution for clarification and further assistance regarding this matter. 

Moreover, you'll want to check this article and learn how to review downloaded bank and credit card transactions: Categorize online bank transactions in QuickBooks Online.

Please reply to this thread if you need further assistance managing bank transactions in QuickBooks Online. I'll keep an eye out for it. Have a good day ahead.