Make sure she's getting enough food. Feed conditioning mash of mix. Make sure her teeth are ok as if she isn't chewing correctly she'll never be in good condition.
Lots of transition work and pole exercises
Proper riding will do the job muscle wise. It will take time, so you need to be patient, but developing a proper frame will do the best job at building up their muscle. Teaching them to push from the hind end, stretching over the topline, and being soft in the mouth will get you there.
I've had good luck with feeding skinnier horses beet pulp for more volume, and rice bran for extra fat. Also make sure they have access to lots of good quality hay. If you're concerned with your horse's weight, I would look into getting the nutrition contents of your hay tested. Despite what people tell you, green hay does not equate to more nutritious hay.
I had this same problem, I have been putting my horse on the walker everyday and been trotting for 4 days of the week this will start to build there muscle more I have also been feeding sugar beet and that has really improved his condition
Try "AniMed Natural Weight Up" I have used it to fill out my rescue, and it works amazingly!! It also supports the health of your horse’s coat and skin. As well as it improves muscle recovery time, and much more that i'm sure you could look into. Lemme know how it works for you if you end up using it! :))