My son was a two way through HS and now in college. It is a challenge for them and adjustments have to be made depending on the circumstances. As far as getting ready for a season it means more attention has to go into the throwing and arm conditioning part of their preparation. This means longer and more focused long toss program, sand ball workouts, more time in getting in bullpens, as well as working on pick off moves. Heavy lifting shifts to Yoga and flexibility development. For a pitcher these have to be done, which means more one on one time in addition to team practices.
For a position player they have to get in their BP, the basic in-outs, and defense work. Where my son got his side work in was typically during BP where there tends to be a lot of standing around. Coaches will accommodate two way players and if they have any experience at all know how to work them into pregame and practices.
For game days it is pretty straight forward, when he started he focused on his pitching warm ups and getting ready to pitch. When his slot came up for BP he took it and went back to pitching warm ups. If he was slotted to relieve he did all pregame and BP only and spent more time in pregame long toss and in close throwing during warm ups.
I would be pretty shocked if a HS coach does not have this down as part of his repertoire. If not the older one can help guide the younger one. There is nothing you can do about the coaching but maybe encourage your sons to talk to him.
