I had difficulty navigating the map for quite some time. Often quests were in areas that I did not know how to navigate to because I was confused on how the map works.

This could be a solution:

You could try going to all known areas where your last quest took place and click on the Duty List > Recommendation > and you should be given all active objectives (quests) available in that area you are currently in. If nothing shows up that means either you have completed all side quests and main quests (in that area of the map), OR you have not reached a required level to progress. Move on to the next part of the map and repeat for accessible quests.

At first I could not even differentiate between story quests and NPC side quests until later on