Yes, I do this myself also. In the data\mopy folder you will need the bash.ini file. If you do not have it copy bash_default.ini which is in there and rename the copy to bash.ini.
The open bash.ini and change this line:
[General]
;--sOblivionMods is the Alternate root directory for installers, etc.
; It is strongly recommended that you do NOT put it anywhere under the
; Oblivion install directory itself, because Oblivion.exe will search through
; every directory under the install directory.
; This "directory thrashing" can then cause performance problems during gameplay.
; sOblivionMods is defined specifically to circumvent this bug by storing files elsewhere.
sOblivionMods=..\Oblivion Mods <--------Change this to
So choose whatever root location works for you with whatever name you want to identify it with.
EDIT: I do not know about your install but I just checked bash_default.ini in notepad and found it one long runon sentance (yes, I have word wrap enabled). I have been using the bash.ini files from previous versions. This could be just me though so will ask in Wrye Bash thread about it. Just don't freak if you have the same issue. You could probably get around it by downloading an older wrye Bash (like 287) extracting to some temporary directory and geting the default_bash ini from there (hope no changes were made to it). I will post more if and when I get an answer in wrye bash thread.