Right, now that it seems I've at last gotten over all my PC upgrade problems I'm finally reinstalling Skyrim. As some of you know my ambitions for my playthrough have finally surpassed the 255 mod limitations (by a long, long way!) and the basic abilities of NMM, so I'm going to install some programs that will get around the game's limitations. I'm going to be installing Mod Organiser and Wrye Bash. Anyone got any advice on how to set all this up properly so it all works smoothly together?

Seeing as you're reinstalling skyrim, you might as well uninstall steam. Then when you re-install, make sure you install it somewhere other then your "program files" folder. Wrye bash says that it can have problems if the game is installed in the default location

- Hypno

If you want the smoothest experience possible, pick one mod manager, not multiple. With multiple you run the risk of one manager screwing a mod installed by a different manager, which when you go to fix that one, screws the first mod install, and so on.

Incorrect.
Just make sure that you use your Mod Managers in this way:
-steam (I'm completely against the workshop, autoinstall, autoupdate?)
-NMM (for fast downloading and installs)
-sort w/ BOSS
-Wrye Smah - rearranging LO w/ hand, if needed, then bashed pazched it
-SUM (SkyProc Unified Manager)
-run SKSE

On a side note, I don't know Mod Organizer.

Yep, got it installed in my Games folder from first time I installed Skyrim. I can't remember who advised it before, but I think it was Gopher.

I'm guessing I install all my mods onto MO just as I did with NMM, but then I merge them via Wrye Bash? These at first will be just clothing, armor, jewellery and weapons mods, because they're the ones that take up the most room. Do I activate them in MO before merging them?

Bash currently merges only a very limited amount of plugins. So if you're planning to go much over the 255 limit, you probably want to spend some time with the CK and TES5Edit to manually mash mods together. Bash is currently not able to merge weapon, armour, clothing mods etc. together; it mostly works for mods changing some small game setting, or a few others.

If Bash merges mods, it merges them into the Bashed Patch. So activate them, Rebuild the bashed patch, deactivate the merged mods.

Ahh, I see, I guess I wont be needing Wrye Bash now after all. Could you link me to any good instructions on how to merge clothing/weapons mods through the CK?

Am I right to assume that I don't even need to upload the mods I want to merge onto MO if I'm using the CK to merge them? I can just keep them in their RAR folders somewhere on my hard drive? Once they're merged I then upload the new merged mod onto MO?

Doing this in the CK is quite time-consuming. http://www.creationkit.com/Mod_Merging might be a start.
With TES5Edit, it's easier - take a look at http://skyrim.nexusmods.com/mods/31458/?. I can't guarantee that it works that way, though.
In short, there's currently no quick and easy way to do this.

Hmm, if I remember right TES5Edit made my armor turn invisible, but I might try it again though, considering I'm reloading everything afresh.

At the moment I'm in the middle of setting up MO. From what I can gather you have to set it up so it recognises the Skyrim launcher you're using? In my case I'd be using SKSE like good ol' Gopher suggested. It's served me well all year so I'll be reinstalling that. I guess you can make MO recognise more than one launcher if you wish, like the official launcher and SKSE?

Rather than try merging mods yourself (which is difficult and time-consuming and can easily not work at all), you might have much better luck posting the list of mods you plan to use. I'm sure that a bunch of forum-goers can look over the list and help you pare it down by spotting incompatibilities, redundancies and such.