yes, Take your balance jan1, subtract it from dec 31 2012, then deduct anything reported on 1099. and declare that as cap gains, if it is futures use the 60/40 split, turbo tax will do that for you when you elect 1256.
what the hell you would do if you trade futures and stocks in the same account I have no idea. That's where tradelog comes in.
If you declare "trader status" and the IRS doesn't call you on it, then you can denote which stocks are long term investments and which are trades. The easiest way to do this is to have segregated accounts for long term investments and for trading. So you get the benefits of long term capital gains if you have a long term investment account, even though you are considered a "trader."
no kidding that's why I keep my conservative investments in one account and a separate account for trading and that among other things was one of the reasons I didn't just put it all in one Universal Account at ib, even though moneywise that would be the best thing for me (providing they don't go bankrupt.)
You could sign up for a separate IB account for your long term investments. As long as the account #s are different, that would be clear segregation of assets based on long term vs short term.