Mmm, that's going to cause you problems. FRED needs to be in the same directory as the FS2(Open) VP files, and FS2Open needs to be in the same directory
tree as FS2. Otherwise you'll end up having three sets of the retail VP files on the hard drive.
I think I see what you want to do though. Try this: Move FRED2(Open) to the Freespace 2 directory, along with the FS2Open EXEs. Place the mediaVPs in a folder under the main FS2 one, say, mvpdata. Now go into the launcher, click the features tab, press select mod and select the directory with the mediaVPs in it. Make sure you have the FS2Open EXE selected.
Now when retail FS2 starts up, it won't find the mediaVPs and you'll be able to play without any problems.
One thing left to do, pilot files (in the data/players/single directory). If you've already run FS2Open 3.6.5+ with your pilot files, unfortunately, you can't unconvert them to retail. If they're still in the retail format (The player files will have the .plr instead of .pl2 extension), make a copy of all the files starting with the callsign of the player you want to use, and rename them so they start with the original name, plus "FSO". For example, "WMCoolmonFSO.plr", "WMCoolmonFSO.Freespace2.csg", "WMCoolmonFSO.Freespace2.css"
If they're in FSOpen format, rename all the current ones to have the FSO prefix like above. Startup retail FS2 and create a new pilot, and play a mission. Exit Freespace 2, download
CSGEdit, and use that to edit the .csg file of the pilot you just created in retail FS2 so that the next/prev mission values are correct. This may take a bit of guesswork since progress is saved in number of missions, with the first mission being 0. (You should be able to open up the mission simulator in FS2Open and count the number of missions)
At this point, if you want to play FS2Open, you select the player with the "FSO" suffix. If you want to play FS2, you select the player without. (Starting up the proper EXEs, of course)
Note:
If you want to play any FS2Open mods, you'll have to use the multiple mod feature, and if you want to use FRED2Open, you'll have to use its mod feature.