Grats on reaching endgame. Unlock Eureka via a quest at Rhalgr's Reach, then it is accessible via boat from Kugane. You can drop out of Eureka at any time and your progress in that zone is saved. It has an independent leveling system so your first goal is just farming enemies to increase your elemental level; you can worry about getting gear upgrades later after you're done with leveling up. When you are high level, your primary way of farming crystals is by participating in NM battles (looks like FATEs, highlighted on map). If you've been completing quests given by Krile then you will be able to access a menu at Gerolt who allows you to exchange crystals for the armor and weapon upgrades that you want. That's the nutshell.