They will appear if you do "New General" in the Commander Interface.
Hope that solved your problem.

Thank you for your tip, the Jedi are going again.
But the clone commanders still don't work when I buy 10 of them, one is in the general selection but the rest aren't and when I add new commanders or generals only the vanilla generals come up

Hm weird. I always got them after i clicked on "new commander" im gonna take a look into the mod. Maybe i can find the issue.
Are you sure you bought Clone Commanders and not officers or basic Clones?

If I buy 10 clone generals or admirals I always only get one added and then no more. Even if I buy more after that I don't get any more and when I go to add new generals I only get generic or vanilla generals.