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Paying Sales Tax in Quickbooks question

Anyone pay their sales tax to their state by credit card and use Quickbooks? I`m having trouble.
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Are your reminders still flagging that you are liable for sales taxes but have already paid for it. A possibility, you paid it through a write check and not through pay bills (vendor menu).
Or forgot to book your payment in quickbooks (use vendor bill pay).
Or have made an adjustment to a prior period in error that have been paid for already (run a query report for previous quarters and see where the liability is outstanding, or run a accounts payable aging report to show you whats outstanding).
When was the last time you reconciled your sales taxes? Are your tax rates correct and updated for each month since you last paid?
Are your sales (revenue earned) correct for each state, create a custom report showing sales by state (if sales are statewide)
With out detail explaination, its hard to pinpoint what may have caused the problem in the first place.
This is why I went to flat rate pricing. It encourages clients to be pro-active and call me before they do something that cost them more money (either in my fees for fixing what they did wrong or in more taxes paid) later. If you like your accountant then you might want to ask about flat rate pricing so you don`t have to sweat calling.