Well, you ought to be able to have multiple mods installed anyway - taking the standard Kingdoms campaigns as examples, each of Britannia, Crusades, Americas and err the other one are effectively mods, each in its own folder.

New mods (assuming made for Kingdoms which most will be other than really old ones) should just create a new folder within the M2TW\mods directory

Multiple copies of the directory might not work well as Windows will get confused about where the game is installed (or rather it won't and will just expect the game to be in the original folder)

Mods have config files and often .bat files or a shortcut that can be used to launch the game with the mod. The config file will have a line like this:

[features]
## enable battle editor
editor= true
## relative mod path
mod= mods/retrofit

and the launch file / shortcut will have something like

cd ..\..
kingdoms.exe @mods\retrofit\medieval2.retrofit.cfg

pointing at the config file

in the examples I checked there weren't absolute references that could be messed up by having several medieval folders but might be worth checking if anything goes awry.

Back to your Third Age issue, is that mod in the original folder or the copy? Moving it from one to the other might be worth a shot

So just installing them normally would work, not having to uninstall them or move them or use the copies? And I installed Third Age in my original and it worked fine until I installed Divide and conquer.

It should normally work - unfortunately I don't know what went wrong with your third age installation (although if you still have several versions of the medieval 2 folder then I do wonder if that has something to do with things)

Divide and conquer is a sub-mod for third age rather than a mod in its own right, so will permanently change the third age mod folder - you should however be able to create multiple third age mod folders (install once, rename the mod folder, install again)

There is a possible complication for all operating systems after Windows XP. Unless you're running the game as an administrator or have played with your settings, Windows will create a copy of the game in its virtual store - this can make save games hard to find and might potentially cause some other issues.

You can find out more on the virtual store here:
http://medieval2.heavengames.com/m2tw/mod_portal/tutorials/vista/index.shtml

or here
http://www.twcenter.net/forums/showthread.php?597889-Installation-of-submods-(-with-pictures-!-)&p=12777400&viewfull=1#post12777400

Great news, I got Third Age to work. I used a different un-adminastrator user and it worked. A glitch involving DAC appeared though. The original 12 factions were there, but they were renamed to the factions they were renamed to in DAC, but it had the original symbols. Also many units were named something weird, that seemed to mean unknown. I forgot what it said, but I'll uninstall and reinstall TA and see if that works. Maybe it's not a glitch, I don't know. I think the original problem was I installed the wrong files for DAC.

Glad to hear it is in the process of being worked out.

Yep, everything is working smoothly with Third Age. But can I still install the other mods normally without breaking Third Age. I could make other users for the computer I use and install each mod on each user if that's not too confusing.

If the other mods are installed correctly (and separately) then they should not break Third Age. They should not even be aware of its existence.

I do not foresee any problem, but my modding skills are basicall RTW and not MTW, and every game has its own unique systems. Caveat given, enjoy your game!

So as long as there is no mod files in medieval 2 folder and all is in the mod folder, I'll be fine?

That's the plan

Most of the files are in the '\data' subdirectory you don't want any mod to change 'medieval II\data', they should all have their own 'medieval II\mods\[mod name]\data' version etc.

How can you tell if mod files are in M2TW/data and how can you fix it. I think that's what happened on my desktop.

Is Broken Crescent modswitch compatible. it doesn't work on windows vista and before downloading it on my laptop i just wanted to make sure.