You can do it different (not sure if exactly easier) than this, of course.
I don't tend to have a clean copy on my system for copy-paste-purposes - there's just not enough room in this box for two of them.
If you don't want to uninstall, reinstall, then copy and
then install all your mods upon the clean copies again, take this approach.
Step One: Rename your current VTMB installation file.
By this, I mean the file you have if you go to the 'Programs' directory and open 'Activisions' (where my PC installs Bloodlines, dunno if this is different for Steam or other systems. I'm using Windows XP.)
There should be a folder named 'Vampire The Masquerade Bloodlines' or similar. (I renamed it, so I can't look it up.) Just open it one time, check if there's the big, fat folder called 'vampire' with all your game's stuff inside, and then go back.
Rename the folder previously called 'Vampire The Masquerade Bloodlines'. It's easy to remain in control of all your installations if you put the mod's name upon it. Example? 'VTMB - CE 1.4.1' or 'VTMB - Companion Mod' or what have you not. This is honestly not a must, but it helps to keep things orderly.
And, if you want to keep it, I'd advise you to rename your desktop shortcut, too, if you haven't already done so. Again it would be wise to put the mod's name on it... after all, you're probably going to have two, three, or even more shortcuts on your desktop after some time...
Step Two: Run the uninstaller.
Don't worry about this step, if you've completed step one successfully (and properly...) the uninstaller will only remove the desktop icon (if you didn't rename it) and the registry entry on your system. The registry entry I mean is the little, bitchy file that tells your PC you already installed VTMB once, and therefore can't install it again. This is also what prevents you from doing multiple installations straight from CD, so this thingie is something you definitely want/have to kick out.
To be absolutely sure that everything went well, I usually restart the copy of Bloodlines after I ran the uninstaller. If the main menu shows up without problems, you did it right, of course.
Step Three: Run the installer.
Pretty much self-explanatory, isn't it? You're doing this to get a fresh copy, so now it's time to install that fresh copy on your system.
If you followed step one and step two and everything worked, you'll have no problems with the installer. After all, you recently uninstalled VTMB, the registry entry is gone (yay!) and there's no reason you can't install it again ... well, except not enough disk space, but that's something I can't help you with.
(Step Four): Start the game once.
I'm not sure if you have to do this, maybe it's mandatory for steam users (this guide is written from the CD/DVD perspective), but just to be sure let the game 'run' until you reach the main menu. If there are no problems thus far, you can close it again - everything went as it should have.
Step Five: Get started with mods.
This is the absolute last step which you probably would've done anyway. Now it's time to modify your game with whatever you please - mods, skins, overhauls, you know what I mean.
I'm sure there are a lot of such guides on the web for VTMB and I'm almost sure that at least one can be found on this board if one were to search long and thoroughly enough (not that more than a handful of people would actually do this, heh), but one more can't hurt, right?
And to be clear about it: This is how
I do it. This is how you
can do it. I don't take blame if it doesn't work with your system and I know that there are other ways to have more than one copy of any given game on your system (yeeees, this works also with other games, at least for me...), so don't mind this post if you don't plan or want to use it.
Happy All Hallows' Eve, everyone.