In my overloaded state I made the mistake of asking google for the best way to install all these new mods I've found. I know this probably seems like a basic question, but I'm really struggling here.

Last time I played was before DB even came out, and I used NMM. I manually installed a few mods because I noticed they wouldn't show up on NMM. I don't know if that's an issue that's been fixed, or if I'll have to go through that whole thing again.

This time around, I have a fair few more mods in my list, and I've heard about this thing called Wrye Bash and this other thing called BOSS...

From what I can tell, NMM is reccommended on Nexus (of course) and apparently Wrye Bash is an acceptable replacement. And some say it's better, but why is that?

And does Boss require a mod managing program of some sort to work? Can you use it with your manually installed mods?

Basically, I think I need someone to tell me in no unclear terms what to do. =/ Thanks in advance.

There are two separate things involved here.

One is management of the installed mods' resources, ensuring that when you remove a mod from your game, all the other mods' content remains. Wrye Bash is probably the best for doing that part.

The other is the correct ordering of the mods esp/esm files, so that where mods are intended to override, they do so. LOOT is replacing BOSS as the mechanism for doing that part.

NMM tries to do a bit of both, combined with automating the download process, presumably to "compete" with the Steam Workshop, because they're competing with Steam as sources of mods.

I personally use Wrye Bash and use it to launch BOSS when I've added a new mod. I'll probably switch from BOSS to LOOT at some point, but right now, it's a question of not fixing what's not broken.

Use Wrye Bash, you can install any mod using that. NMM has some limitations. Besides, your going to need Bash anyway to make the Bashed Patch to get all the mods to work together.

You want to begin by watching this series of videos by Gopher, they explain a lot: https://www.youtube.com/playlist?list=PLE7DlYarj-DdhDG41roBVJfNCqvO5MmKP

Then you need to make a choice what mod managing tool you want to use, and you have three possibilities, NMM (Nexus Mod Manager), WB (Wrye Bash) or MO (Mod Organizer). The NMM is the simplest of the three, which doesn't mean that it isn't a good tool to use. It does it's job it is supposed to do and if you use NMM you will safe a lot of time in comparison to manual installation. MO on the other side is a more advanced tool and comes with fancy things like mod isolation, profiles, a virtual data system, etc, ++ .. it is better, but also a bit more complicated to learn. WB is a longer time around and widely used for modding Oblivion as well as Skyrim, it is also THE tool for creating "Bashed Patches". If you want to know more about Bashed Patches, I would suggest to read http://www.nexusmods.com/skyrim/mods/36189. Long story short, if you use NMM or MO, you still should use WB aswell for the mentioned Bashed Patches, as NMM/MO can't create them.

BOSS is the tool of the past to manage your loadorder (and it is standalone, you do not need a mod managing program like NMM/WB/MO to run it). That said - a few weeks ago it's spiritual successor was released, called "LOOT" (Load Order Optimization Tool) and therefore I would suggest to use LOOT instead of BOSS to sort out your loadorder. You can download it http://loot.github.io/, and you should watch these videos (they are also in the playlist of the first link):

https://www.youtube.com/watch?v=YzsBKYUrcbE

https://www.youtube.com/watch?v=SzoyWugzZAw

Been using Wrye Bash (and its Fallout ports) since Oblivion. Haven't really felt the need to even try switching to anything else.

Sometimes you need to manually repackage things you download, and it isn't the most obvious or user-friendly.

But the payoff if you will always know exactly what is overwriting what and can easily switch back and forth by juggling your install order and annealing.