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I'm looking for some best practices for changing the deposit account used when someone does an online payment to an invoice.

I've found in the payment app where it searches the paymentgateway table and tries to grab the DepositToAccount - RecordID, is it safe to just update that table record or is there a better way to update it?

Hi,

You can definitely do that but that would make that account the default account. You can also update it with the name by using this field DepositToAccount - Display.

-Inder

I've updated the field, but it did not seem to make a difference. Is there something else I need to update along with it?

Assuming the workflow you are referring to here is when the customer is trying to pay an invvoice from the portal.  There are some conditional statements in play here. It first looks for AR account and the last used account. If it cannot find then it looks for other variables. So you might want to check these actions and see if you are fulfilling those conditions. 

Hope this helps!

- Inder