I am clearly late in the year and have just opened a QuickBooks Online account. I already had invoices paid for this year... My question is; would marking these as "paid" have an impact on my balance with bank account, being that the customers have already paid?
yes it would, either the bank account would increase if you have it set to automatically deposit, or undeposited funds would increase. At some point undeposited funds needs to be deposited to the bank account too
Best option IMO is to match the deposit you received when paid, to the invoice
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