In short, somehow I seem to have been losing the main quest. 

Assuming the main quest is the one(s) followed under "Story," I sometimes have no quests except for a single one from the black spirit telling me to level up to the next level. I went online and found a quest I had missed and went back to get it and it turned out to be a "Story" quest but I would've never found it without going online. I'm wondering if there are other story quests I've missed or how I can know in the future if I've missed an important quest along the way.

I'm still fairly new to the game, but from what I can see, the "story" quests aren't the main quest line, they just seem to be more of an extra quest to go along with the black spirit quests which seem to be the main quest line, at least from what I've experienced so far. 

Story quests are just story quests they will lead to knowledge n other items and if u read them give more lore on the world monsters and npcs. If u are referring to "main" quest that will be the black spirit quests that has the diamond swirl logo. Story quests have an open book logo.the black spirit quests are level locked. Believe me u do not wanna get to mediah at 45 n under geared lol. So when it sayes to lvl up then lvl up and the main questline will be available to continue ie black spirit.

If you press r2 in the quest menu it has the main story there, it it’s listed from the last quest you done till the first,, I found this out last night because I lost track of the where npc for the main quest was due to a boss fight.