Really, the only way to upgrade is to buy new armor. You can find an armorsmith to craft a new suit, or you can do a vendor search.
If you want a full new suit by doing a vendor search, search galaxywide and look under Misc./Wearable Containter. That way the full suit will be listed and can be bought instead of having to buy it piecmeal.
The other way to upgrade is if you have crafted armor. Look at the armor in your inventory. Any crafted weapon, clothing, or armor that is listed with green words has a socket available. You can find an armorsmith who can then place modifyers into those sockets. It won't change the armor value, but would give you a skill mod.
Unfortunately, there is no way to upgrade an armor rating. That is, you can't take armor with an energy of 3000 and upgrade it to 5000. For that, you just have to buy new armor.