Here is a very helpful thread: HorseHelp: Building up your horses back, In-hand and Under Saddle
As for your horses in training, fitness building exercises. Hmm. Trotting helps with building muscle in the hind end, as does riding up hills and laying down some poles flat on the ground. Just be careful. I wouldn't worry about building fitness, I'd focus on just slowly teaching them how to be ridden, how to yield on the ground, how to relax, go through the paces (eventually) and over time, they will become more fit as they learn and then you'll be able to do more with them.
For your appy who I assume you can do under saddle work with.. lots of transitions, changing gaits, lots of figures (weaving, circles, figure eights, serpentines, etc.) and hillwork are invaluable. Working on a forward walk, a trot (posting on the correct diagonal if you do English which will help stretch out the horse's shoulder) is very beneficial for muscling a horse, and cantering helps with balance and some other stuff I haven't figured out yet as I've just now begun to canter.
It's important to change things up no matter which horse you're working with. Doing the same thing without doing more or doing something different won't make much change in your horse and possibly make them unexcited or unmotivated to be worked with. Capture their attention and focus, keep them thinking.
That's what I think at least.