I am a complete Linux noob, but this is how I do it
My O.S:
Arch linux, latest kernel, free drivers, really low resources PC,
1- Install wine. (with all its dependencies if you're a paranoid like me).
Open your terminal and type sudo pacman -S wine wine-mono wine_gecko winetricks
or
Search "wine" in your favorite software/package manager. (I mean ubuntu/linux mint software manager, octopi, etc)
2- Open your terminal, type winecfg (wine configuration) to... configure wine. But you dont have to configure anything, actually. This screen appears.:
You just can click "Accept". On the tab below you can choose which version of windows you want to use. The default is windows XP. I use windows 7 just in case. 32 bits version. Unfortunatelly wine can not handle x64 yet.
This is what wine has done (select "see the hidden" in your file manager)
Now you have a C drive where you can install anything you want (more or less).
3 - Insert your Medieval total war disc (steam users, unisntall steam: Steam is evil). Now you can see this
(The disc inserted is Kingdoms, but come on, imagine its Med 2 first disc). Right click with your mouse on the setup.exe icon, select open with - wine. And... installation begins. The sega installer automatically points to the right place (In my case:/home/antonio/.wine/drive_c). (antonio, because thats my name and thats the name of my directory. In your case it may be /home/soren/.wine/drive_c or /home/marcus/.wine/drive_c, I dont know, how would I? Remove disc 1, insert disc two when requiered, click accept to "install drivers", or update or whatever (do not worry if a message appears saying a fault has occurred), and Medieval 2 is installed on your linux OS. Now do the same with Kingdoms (please). Kingdoms installed? Fine. Updated to v. 1.05? Perfect.
Now, to check that everything is in order, I usually start a kingdoms campaign (crusader, teutonic, whatever: remember you have to install one of this campaigns to create the "mods" folder in your installation). I mentioned that my computer sucks and I use free (non-propietary) drivers, but anyway I can playperfectly with medium/high video options and normal units size.
Now, to prevent problems that may arise (this is a advice I've read by some modders) lets copy the SEGA file we have here /home/antonio/.wine/drive_c/Program Files (x86) here /home/antonio/.wine/drive_c . Its just a copy-paste, takes only a few minutes, and a prudent man is worth two. (Literall translation of a spanish saying).
4 - Eeehh... you should download the mod you want to install.
5 - You have downloaded your mod (Three .exes in this case, TATW_3.0_Part1of2exe, TATW_3.0_Part2of2exe and TATW_3.2_Patch.2exe). Right click on your downloaded TATW_3.0_Part1of2exe, select open with - wine and start the installation, BUT, be carefull, mon amie, because the installer will point to program files (/home/antonio/.wine/drive_c/Program Files (x86)/SEGA/Medieval II Total War) and we want to install it outside program files (thats why we copied it before). All you have to do is delete the underlined words (/home/antonio/.wine/drive_c/Program Files (x86)/SEGA/Medieval II Total War). Now, installation is pointed at the right place /home/antonio/.wine/drive_c/SEGA/Medieval II Total War. Same thing with part2of2exe and with the patch. And there it is: Third Age Total War installed and working on your PC. Click the icon created on your desktop or search in your desktop menu, and play.
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The process is really simple, may not look so because of my difficulties with this language, my relative ignorance about linux (probably I have used the wrong phrase or term here or there) or simply because I have not known how to be clear and concise, but I assure you: Installing Medieval 2 (the good old windows discs), with most mods (I have had problems only with one, I will try again to see what happened) on linux is something really simple and brief.
Of course any correction or addition to the "guide" above will be welcomed.