Gems of the relevant slot (to each relic) can be equipped by going into a relic and clicking on the gemstone shapes at the bottom of it:

i

This relic can have one square & two circular gemstones attached to it by clicking on those shapes at the bottom of the relic.

thank you

by the way how do you get relics and gemstones in the first place?

Mainly Chimera, though relic forging materials have shown up in tournament rewards now - as well as the new event relic being the top reward in the Event Dungeon tournament. There will be other sources in the future as well - including live arena.

thank you