I have no idea, really, how the QSBS aspect might play into the AMT aspect, or it it even does. But you are right, you can't deal with both aspects in one fell swoop using TurboTax.
Here's one approach you could use. (This assumes you're using a desktop version of TurboTax where all the Forms, Schedules and Worksheets are always available to you.) Enter the sale using the ISO "guided" interview. Then go look at Form 6251 and see what adjusting entry has been made on line 2i. Write that down.
Then delete the trade and re-enter it using the regular 1099-B interview, taking the path that asks about the QSBS aspect. That will get that "side" of the sale for regular taxes taken care of. After that, go and work through the AMT interview. That interview will ask about the adjustment needed for the sale of the stock acquired via the ISO. (HOWEVER, I just tried to do that using the AMT interview and it looks like there's a bug in this part of the program. I posted about the problem so, hopefully, TurboTax will get that fixed.)
