Okay. There's only one right way to do this. Put everything you've done into ONE folder, i.e. merge all the different data folders you have created into one, put it into your own modfolder, and created a mod.ini which references the mediavps:
[multimod]
secondaryline = mediavps;
If you want to FRED using that folder, create a shortcut to FRED, and add "-mod <your mod's name goes here>,mediavps" in the target field.
Also, take a look at this wiki page. It tells you exactly how the data\ folder structure looks like, and what files go where.
mod.ini files are recommendable for a finished, distributed mod, but they have their pitfalls and personally I simply use the manual -mod Mod1,Mod2,Mod3,...,ModN command line.
I agree that you should keep your creations in as few places as you can. I also strongly suggest you abstain from putting
anything at all into the following directories:
..\FreeSpace2\data\*\
..\FreeSpace2\mediavps\data\*\The reason for keeping things out from root data directory is that the game ALWAYS reads that directory. Putting stuff there will eventually make you a victim of a rogue table or something similar and then you and everyone trying to troubleshoot will be scratching their heads when you can easily avoid the problem by never putting anything there at all.
Same is true for the mediavps\data\ directory; you can do it, surely, but it's much easier to troubleshoot MediaVP issues when the data directory there is clean. You can do it, just don't expect support and warm fuzzy feelings from FSUpgrade team.

For these and other reasons, you should create a mod directory for your stuff, ie.
..\FreeSpace2\RazialMod\data\and put appropriate sub-directories in there, ie. models go into
\RazialMod\data\models, maps go into
\RazialMod\data\maps, effects into
\RazialMod\data\effects, tables into
\RazialMod\data\tables etc.
Then, either put in a mod.ini file that activates mediavps when RazialMod is activated, OR (as my personal preference is), locate the Custom command line in the Launcher's Features tab, and type in
-mod RazialMod,mediavpswhich does absolutely the same as the mod.ini file with the exception that you immediately see every directory that you are telling the game to read.
Personally, I'd like to add that I often make a specific mod directory for specific stuff. As a result my -mod command line is sometimes a rather long string of directories, but I haven't noticed any adverse effects from this.
An important thing to realize with the file structure is that VP files should only be a distribution media, as in a container for your mod directory. The VP file has the exact same internal structure as any mod directory; it has a data directory and appropriate sub-directories.
Also, this thread could be moved (or split) to FreeSpace modding, as most of this stuff has little to do with FREDding (as in, mission building) and more with general modding. But I'll leave that for the FREDding forum mods to decide.
