If you hover over a Gregtech machine in NEI, or right click it with a Gregtech scanner it will display several letters, for example: O B T M
These explain which upgrades you can use, O for Overclocker, etc. To insert an upgrade, simply right click a machine with it in your hand and, it will poof into the machine. As a warning, I recommend a transformer upgrade for all of Greg's machines prior to adding overclocker upgrades. They'll draw a tremendous amount of power by the second or third upgrade.