You probably should still understand that there is a difference between missions and quests.

Missions you will get from a gate guard usually and will show up under your mission log. These improve your national rank. Later you will have missions that start elsewhere but by then you shoud know the difference between missions and quests.

Quests are just random... erm... quests. They will show up in your quest log. Keep in mind that these are very different things.

Also in the future you could check the link sticky and try a few pages there such as MysterTour, Somepage or Allakhazam for good info on quests as well as KillingIfrit and a few more for good info on missions.