Agree with the general consensus in that (a) I'll support whichever option you choose, but (b) if you are looking for opinions, using the base salaries would be hella-easier.
I also had a few questions about enforcement of the cap. Is every team responsible for self-reporting their cap hits? What happens if somebody doesn't do that? Let's say a team is $2M under the cap, but we realize halfway through the season that they are rostering a player listed at $1M in Fantrax, but who actually has a $5M cap hit. What happens? That example could involve getting mad at the person for not checking, but what if they did check a cap site and both the site and Fantrax were wrong? What are the repercussions? Also, what happens if a team trades a $2M cap hit player for a $6M cap hit player halfway through the season, which puts them over the cap? Who is policing that? Also, would there be a pro-rated cap for a half-season of these players, or simply the full cap hit?