There should not be any difference between your broker's official 1099-B, and any sales records that you've kept separately and manually, as long as your cost basis, net proceeds, holding period (short term or long term) and type of transaction (covered vs. uncovered) match. In other words, if you entered, say, (4) stock sales separately using "Capital Gains Worksheets" or whatever, and the sum total of those dollar figures equaled the equivalent data from your 1099-B, then it makes absolutely no different what the source of your data was -- the net tax result is the same.
However, for purposes of correctness any complying with IRS rules, if you have just a few (example 4) stock sales to report, then we would recommend entering each of them separately in the program, through the regular interview mode.
I've attached a screen shot to show you where you would begin each entry in the Interview Mode. Note that if you're using TurboTax desktop, then you could alternatively make your entries through the Forms Mode. Is that what you mean by the expression "Capital Gains Worksheets?" If it is, then please know that either way will give you the precisely equivalent tax results, provided that the data is input correctly.
