I have an Excel spreadsheet that I use to keep track of all checks. The stubs don't get filed away until I've entered the totals under the correct sponsor and month.
I use Quicken for tracking my checking and credit card accounts. I almost never pay cash for anything business related. The key there is consistently entering all transactions, and using the appropriate expense category.
I sat down with Turbo Tax last night and completed my Federal taxes in about an hour.
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