Toddmc nailed it on the head. In my experience, the most important aspect of bass drum playing is your leg angle. If it's not sitting at just past 90 degrees, you're losing speed, strength, and stamina. Make sure that you're adjusting to accommodate that.
As far as heel up or heel down, it has to do with preference, playing style, and possibly the song. Don't think that learning one now will keep you from using the other! I started of playing punk rock and used a heel up technique but I found that my legs got tired pretty quickly since I was new. I spent the next couple years playing funk and some contemporary music (mainly because its what I could find a band for) and trained my heel-down playing. Strengthening that "shin" muscle has really helped my stamina and consistency. Once again, I changed styles and did some Hard core music, which almost requires playing heel-up. (Some people can do incredible double bass heel-down, but the majority sticks to heel-up).
Now when I play, I sit with my heel on the pedal and play like that. If the song gets bigger, I might bring my heel off. It really just has to do with experience and what's comfortable for what you're playing.
So don't stress! Just keep playing and take a whack at the other one every now and then!