How to exercise to deal with the body aches?

Slowly & surely. Exercise is generally good for achiness, but start slow - warm-up, low-impact aerobic work (bicycling, elliptical), easy stretching once warmed up, light weights. Try to exercise on most days of the week - consistency is important in this regard.
Depends, but ... Yoga or stretching when done properly can be helpful for body aches. Before doing either make sure your muscles are warmed up -- walking is usually a good way. If you do stretch, hold each position for about 30 counts to the point of discomfort and don't bounce. Bouncing will work against what you want to accomplish. Try stretching 15-20 minutes once or twice a day.

Related Questions

How to exercise and deal with the body aches from bad posture?

See below. Work with a physical therapist or a yoga therapist. Both are trained to help people correct muscle imbalances that can result from poor posture. Read more...