Since you're just getting him back into shape, I would suggest lots of walking, but it can't just be ambling along! It should be a forward, energetic walk with the energy coming from behind. I would probably do 30 minutes of walk, 5 minutes trot, 20 minutes walk, 5 minutes trot, then finish off with another 10 minutes of a good walk before letting him cool out. When he starts getting into better shape start increasing the trotting time and decreasing the walking time (slowly). Hills are always a good thing as well.
Right now my horse is finally getting back into good shape so we do trot sets. I'll take him out and do anywhere from 30-45 minutes of trotting up and down small hills and asking him to start to accept the contact and lift his back. The hills help with that because he really has to come from behind. When I do a good day of trot sets I'll usually give him the next day off, check his legs, maybe hand walk him some, then resume my flatwork schedule the day after that.
A lot of horses really enjoy getting out of the arena for conditioning and will go at it with gusto. I know Willie really enjoys it and always comes back to his arena work with a much better mindset.
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