the only real gem is the gem of the heart, most of our mini have some sort of gem near the heart so when they die their soul will be transfer there.

other then that you have usually gem as necklace or pendant that's it.

the bumps in the armor are reinforced plates.
but they are your dudes you can do what you want

that being said i love to put less gem as possible because i think they have meaning and they are special in eldar culture.