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If you are paying via EFTPS or whatever the heck they call it, you can just change the check number to EFT or some such and leave everything as is. Be sure to save a PDF copy of your payment confirmation. I keep a folder titled Quarterly Reports and keep a copy in there with the appropriate name (2009Q1EFTPS Payment).
I have no experience using QuickBooks ePay service if that is what you're referring to.
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"My clients’ wishes are the center of my attention." -- David Guido, a contractor in Woodstock, N.Y.
New York Times, July 20, 2006
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