To customize a Gem Unit select Customize in the main menu and select Gem Unit in the screen after. Here you will be redirected to the character select screen layout which will allow you to select the character in which you want to edit the gem of. Every character has preset loadouts each with 2 gems equipped. Select a character and you can either add to it by highlighting the blank slot and selecting a gem with from the load out or you can even remove the gem by pressing , after you are done customizing back out with and your achievement should pop up.
When obtaining this achievement use this time to set up gems for your Arcade runs and your technical achievements. You may even see yourself coming back here when you are trying to complete the 20 missions for "Mission Specialist".