I'v e never really been quite sure of the 'proper' way to go about adding and removing mods to an existing game. As of now, I have all my new towns, villages, etc. as well as all my replacers, tweaks, and sounds added (what i wold consider the base adds). I also included some dungeons and quests fit for a fairly new player. As far as the quest or dungeon mods do I only add the higher level dungeons/quests when I reach those levels needed to complete it? And if I finish them, am I supposed to remove them from my game to clean it up a bit? And if so, how would I remove something and keep any items I found within (or do I not get to keep them?)?

It is best to add all the mods you'll want to play before you start.
Removing a mod when you're done playing it is not recommended unless you know what you're doing. Not only will you lose all the items from the mod, you're going to get problems with missing references.
If you do need/want to remove a mod mid-game, be sure to update and repair your Save with Wrye Mash. (and recreate your Leveled Lists)
Having the MW Code Patch installed will also help prevent problems when adding/removing mods, but it's still a good idea to use Mash to be certain your Save is updated.

And if you want to remove a mod but keep the items you gained, you'll have to make a new ESP that only contains the items you want, then deactivate the original ESP.

Adding mods mid-game is simpler. Just be sure to recreate Merged Objects and Leveled Lists just in case. (and update your Save with Mash)

Removing or adding mesh/textures replacers is almost always going to be safe, since they hardly ever alter or create any references.

I see. Well there's some mods that are for higher levels that i've left out for now. As far as just removing something that adds creatures (like More NPC's or Dogs Of Morrowind for example), it seems pretty straightforward using Wrye Mash. I wouldn't want to attempt removing any quest mods during the game. I'm not all that familiar with making my own .esp and all that. At least now I have an idea how to go about doing it.


Edit: So as far as merging leveled list, I use Wrye Mash which does the job very easily. I use TESTool for merging objects, and Mlox tells me which mods to exclude from this merging (if any). When I do these things, I just keep everything active (unless told not to) and create my merged level and merged object list. Is this a good way to go about doing this, or should I be more specific in my mod selection?