I'm not clear about what you mean.
You must have the JSGME Mods folder placed outside the cfs3 directory, and then the file structure needs to point from there down to the final location one subdirectory at a time to where the included files should be specifically deposited. If you don't cfs3 will see both the old and new files when it starts and get confused.
For Example:
If the program is here C:\Program Files\Microsoft Games\Combat Flight Simulator 3
Then create C:\Program Files\Microsoft Games\Mods
Specific Mod folders would look something like this C:\Program Files\Microsoft Games\Mods\Name of Mod\Combat Flight Simulator 3\Aircraft\Name of Aircraft To Modify\Texture\replacement files go here
The first level of folders within the Mods directory is where you name each collection of files that you want JSGME to install as a set. So perhaps you want something like:
New Shaders - Korea
Custom Weather Pack - Korea
Hollywood Explosion Effects - Korea
New Shaders - MAW
Winter - MAW
Spring - MAW
Summer - MAW
Fall - MAW
These are the names that JSGME will display in the box on the left side that you select. Once you tell it to install each Mod these names will be transferred into the box on the right of JSGME.
For those more advanced users that may be reading this you only need to install one instance of the JSGME program on you computer, even if you have multiple versions (CFS3, FirePower, MAW, PTO, ETO, Rising Sun, etc.) installed on different hard drives. All you need is to create multiple desktop shortcuts to the program with the "Target:" set to where you installed JSGME (for example S:\JSGME\JSGME.exe), and the "Start in:" set to the directory where that particular MODS folder is placed (for example "F:\Program Files\Microsoft Games"). Name each shortcut so you can tell which group of installations it will be serving. I have WW1 and multiple versions of ETO customized by era on one drive, PTO and Bob on another, MAW and Korea together separately, and then All Jets, Fire Power, Rising Sun and the Base Install on the C drive. JSGME will create local copies of the JSGME.ini files it needs to keep track of what's installed in each location. DO NOT DELETE OR MOVE THESE OR YOU MAY CORRUPT THE GAME!