You're not wrong...the quest lines are confusing for new players, and the game does a bad job at explaining the progressions. I will not spoil anything, but based on what you've said you've completed let me break down the various quest lines:

1. Main quest line: you've lost your soul, there's this prophet recruiting you...welcome to the main story line. You are allowed to proceed through this line every ten character levels. Each quest awards a skill point and boring exposition. Quests always spawn at the Harborage until they start spawning one after the other to the end.

2. Three faction main quest lines: while molag bol is bol-ing about, a civil war has started. Originally the leveling system kept you in the right area, but with One Tam you can do them whenever, or all at the same time...thus the confusion (partly).

The faction stories proceed through each zone in that faction in order, with each zone containing 4-8 major quests in the line. So for Daggerfall: Stros and Betnik (although the game allows you to skip the "starter zones" in any faction...they're mainly designed to help players totally new to gaming), then Glenubra (zone 1), Stormhaven, Rivenspire, Alik'r, and finally bankorai (zone 5). Generally, these quest lines always have a new quest giver at the previous quest turnin. In other words, you finish a quest and an npc with a marker runs up...that's the continuation. There are many, many skill points in these quests, but only at major milestones.

What can add to the confusion is that you can pick up the first quest in a zone even without completing the previous zones. For example, if you travel to the entrance to Rivenspire you can pick up that line, even if you haven't done Stormhaven, and even though stuff that happens in Stormhaven informs the Rivenspire story. Therefore, it might be helpful to refer to a list of sequential quests if you get lost:

http://www.uesp.net/wiki/Online:Daggerfall_Covenant

Not a lot of good lists exist. That one appears to be a pretty complete list of only Daggerfall faction quests.

3. The guilds have quest lines. So....sigh...great. Quick breakdown. Mage Guild levels by collecting blue lorebooks, and this opens these quests. Fighters Guild levels by killing undead and daedra and dolmens, progressing that line. Undaunted has an intro quest then then eventually guides you to group dailies, but no quest line other than an intro.

4. DLCs: Craglorn and Wrothgar are their own mega-dlc self contained storyline zones. They all have their own storyline and many, many other quests...with the stories being independent of everything else in the game, mostly. Dark Brotherhood and Thieves Guild Are smaller, self contained DLc zones with progressions with 6-8 skill point quests as you level those lines. And Imperial City has a quest line.

5. A gazillion, bazillion side quests. They're all over the game. A tiny fraction award skill points (maybe 3-4 side quests in the whole game). Play them or skip them...you won't lose out on anything essential.

Tip: the map icons are black if there's still a quest or activity there to complete. Once they've cleared, they go white. If a town's map icon is a little black hut, there's a major quest or quest line in that immediate area.

So, how to do it "right?" The game is designed as a sandbox...you can do everything in any order you like, but that can make the narratives utterly confusing. If you like the stories and want to experience that aspect, I recommend starting in zone 1 and playing through that quest line. When the npc sends you off to zone 2, either go back and play the side quests if you're having fun, or move on. Play the guild quests either as you open them, or save them to do in order - mage and fighters are designed to be done one per zone as you level.

ESO stories are very convoluted. Feel free to travel to other factions, but I don't recommend trying to play multiple main faction quest lines unless you're very good and making sense of this stuff. And they barely make sense if you play them in order.

If you're wondering about chronology, at a point in the main story quest the prophet will ask you to speak to three leaders. This occurs immediately after the three faction quests end, and right after the final fighters and mages guild quests. This is where all content in the original release converges. However, in the original release you played one faction to this point, then moved on to a showdown. The game "ended" and you were invited to see how things looked from the other factions' points of view. With One Tam you can play through the factions before ending the story, but if you were to play all three faction lines before the main story ends, you'll be waaaaaaaay into vet levels before you meet Molag Bol. DLC stories take place after the main story and faction quests end...generally in the order these were released, although the stories aren't dependent on the original game content.

Yes, it's overwhelming, lol. Hope that helps...have fun!