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How to get bank deposits and invoice payments to only show once?

I set up my account to download my bank statements, but now I have all my payments noted in my account twice - once when my assistant puts them into the invoice as paid, and then the deposit made to the bank that downloads with the bank information. How can I fix this? Do I just have to delete any deposits? I am hoping to somehow reconcile the deposits with the manually inputted payments, to make sure they add up . . .
 
sad I’m confused
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