But honestly, you can't expect any software to guide you through everything.

When I come across something unfamiliar, whether or not the software will do the fancy calculations automatically, I'd always read up on the instructions (like in the good ol' days) and do a bit more technical research.  The output can only be as good as your input and there could always be a couple more switches you need to flip for your particularly situation before the software will correctly prepare the return.  I can then verify that the correct logic has been applied and that the return is technically correct.

If I'm wrong after all that due d, so be it.  But if I didn't do my homework and the return turns out to be wrong, I can't go back to blame Intuit or tell my client the return is wrong because of the software I use.