You should expect a degree of soreness when you start working out again. In time you'll get use to the weights. But resting muscles is a key component to growth.

Yea, you should partition your workouts to ensure proper rest, doing upper body one day, lower body the next.

If you wanna be really serious, you can cycle it even further like this:

biceps/triceps
chest/lats.
deltoids/traps.
quads/hamstrings/glutes/calfs.
and repeat
throw in a few ab workouts there. Once or twice a week, don't work-out at all, and do some running instead.

The formula is really simple. Work out. Eat. Sleep. Repeat.