Watch the Physical Position online guitar lesson by Bruce Arnold from Guitar Physiology Survival Guide
How you hold the guitar is crucial to good guitar technique. I recommend standing up when you play. This is how you will perform most of the time and it will help to insure you don't run into many of the problems that occur from sitting down.
When using the standing position your weight should be evenly distributed between both feet. Be careful not to slouch. I've found it's best to wear shoes as you practice to give your feet support. It also is better to stand on a carpet rather than a hard floor. If you are going to sit then I recommend the classical guitar style of playing with your left foot up on a guitar footstool and your guitar across your left leg. This will keep your guitar in a similar position to when you are standing.