Vinigar,
You are right on the 4797 for your trades. I am assuming when you enter in the system that you can keep adding trades that will then print on supplemental sheets.
I use Kiplinger software to do my taxes. I am not sure it will handle shorts or other transactions any better than Turbo Tax. For instance I had a ton of options that I sold last year that expired worthless. Even though I coded them with an X for expired option, the system flagged every trade for a cost basis.
One solution may be to use Excel, I use IB and see they have an export to excel option. Im still on yellow-tablets myself, but you can do some pretty useful stuff with a little excel talent.
I will set up a dummy return or try to with Kiplinger, including some business expenses. I will see how it flows and post the results. You may want to try the same with turbo tax. Look for it on Friday night, since I have been kicked to the curb for the evening.
I looked at the green trader website, and have seen several posts of other traders recommending them. All in all it looked like a decent site with some sound advice mixed in with some promos.
I don't know the cost of the software, but it looks like Barrons has done a review. That may be a viable option depending on your situation.