It's really simple, follow as shown below
Go to your program files and locate the installed folders for Rome total war.
It should be named either 'Activision' or 'The Creative Assembley' (depending how old your RTW game is)
Once you opened it up it should read 'Rome - Total War' literatly right click and copy it and paste it in the window opened. If asked to replace existing files and folders click no.
It should after being pasted look like Rome - Total War(2) or Rome - Total War copy and there you go done and dusted.
depending how many mods you can copy it more then once but make sure they don't have the same name!
When you want to play the game from your copied folder incert the cd and go into the folder and click the shortcut to launch game it should load the game to the files existing in the folder. So thats how you get your vanilla and mods without having to un-install all the time to play a different mod.
Hope that helped
Further more if you want to install a mod to the copied folder you should select the copied folder in the installation process when the installing the mod. (please note not all mods may have this option so keep an eye out when installing if you don't get prompted to choose it's installation destination, because it will automatically install to your vanilla original folder.)