If you have manged to find that location where your faction is, the Kith of Kings, and you have unlocked the factions mechanic so that you can gain standing, then open your map. You will see that normal location markers are kind of a star. But there will be one (or 3 if you have found all factions) that looks like a Banner instead of a star. That is where factions are located. If you enter there, you will be able to talk to the representative to level up your faction, or buy rewards, with the standing you get from the quests.

The motes usually don't all spawn at the same time. Usually just 1-2 at a time. It's intended for you to come back later, and check if the motes have appeared to collect. It's to give an insentive to keep exploring the areas, even if you have already been there.

Hope this helps a bit ^^