I'm not going to give advice because although I work out a lot, I'm not really qualified to do so. But I would like to congratulate you on making the decision to go out and do something. It can be hard hitting the gym, especially when you don't really fit in there body type wise.
Ok well, I will throw in my two cents I guess. I personally like to do as much with free weights as possible and avoid using the machines. I feel I get a better workout as I'm constantly responsible for the weight and the machine never helps me.
If you want to get more lower body stuff in there, one easy and effective way to do so would to be start doing squats. These are great, just might be my favorite exercise, and give your entire lower body a good workout. If you do start, work with very light weight at first and perfect your form. There is almost nothing more frieghtening to see than a guy loaded up with heavy weight doing squats with bad form. Very dangerous.