Just flip a coin...whoever gets LT automatically wins.
Probably the easiest thing to do is just each of you own two teams. You might have to play around with the roster settings or maybe keep weekly rosters in Excel or something. (Just let the website score the players, then copy the scores of the 'active' players into your spreadsheet and tally the total score that way.)
I've never seen a two-team league, so that is the best I've got.