When I tried to do mine manually I found that some of the boxes that had amounts were irrelevant to the process. I did autofill on my second try and the amount owing changed by a mere .40 cents 

Thanks. It turns out that the numbers in all the boxes do get put into your form - BUT the TurboTax pages for that information do not always show the numbers or warn you not to put into the pages any numbers that are also on the T-Slips.

I double-entered my capital gains and investment returns, producing a large amount more tax than I had been expecting! I caught one of those errors before filing (well worth the $45 for their expert review, though probably the CRA would have noticed) and the other after filing so sent in a revised return wihtin a day.

BTW if one makes the changes on the TT forms then try to file a Revised return, the revisions will not be marked as changes from what one filed originally, so the assessment notice from the CRA will not reflect the changes. I am counting on the CRA noticing the difference on its own, or i will give them a call in a while about it...

CRA advises that all AFR download entries should be checked before accepting them into your return. After accepting information, check all T-slip entries before you file.