Did you play through skyrim without mods before adding the mods or did you ad them right away?
Depends mods can be "lore unfriendly" but you can find lore friendly mods i would recommend using http://www.nexusmods.com/skyrim/? and their nexus manager.
It's more dependent on you when you want to add mods but the nexus is a great place to start.
Helpful links for modding skyrim:
https://www.youtube.com/user/GophersVids
Great Modding tutorials including the best SKSE installation guide.
http://skse.silverlock.org/
Skyrim script extender (does what it says and many advanced mods require it)
https://boss-developers.github.io/
Sorts skyrims load order and is essential when your mod list has become quite long.
http://www.nexusmods.com/skyrim/mods/1840/?
Shows what mods might be incompatible and can show what mod another mod is dependent on.
I have not used Mod Organizer but you can look into that yourself if needed.
(hope this answered your question somewhat)
Happy modding.
I played through a couple hundred hours on PS3 so no mods. Modding skyrim was the only reason I got into PC gaming really.
Played through a couple years back on xbox 360. Now with mods on PC, it not only looks like a brand-new game, but it also feels like one. Could not believe the difference in visual quality/realism at first. I still just stop and look around while playing, just to admire the view. Vanilla skyrim look horrible to me now. lol. Now I actually want to take my time going through the game (no fast-travel) just because it looks so good and plays better (combat realism mod - hardcore mode). Oh and butter-smooth 60fps is soooooo nice! ;)
I played about 300 hours on my PS3 and oh how fun it was, and it wasnt until I got into PC gaming that I repurchased it and modded it now I have currently 160 mods running and I cant imagine it without them as it looks incredible and is so much more immersive and improved over vanilla, as for your first playthrough I would only really reccomend bug fixes and graphical mods, so you can experience the game as is, and then mod the hell out of it.
To fully appreciate how much the mods improve this game, in terms of both visuals and immersion, you should at least play through a good chunk of the game without any mods, for sure.
https://www.youtube.com/watch?v=6Kba2AfNRXM From Logan's gaming channel, watch it.
not sure how you managed to not have played skyrim at some point before now, but play it vanilla first, then add mods later. That way you know how you want to mod it better. Only you know how you want your skyrim to be, so only you can decide what mods to add.