My idea of a decent editor:

The way i figure it, the tree on the eft could be set to a specific directory (but defaulted to $mircdir). From there, you can right click in the tree, and select either new dir, or a new remote file. The folders shown would be sub directries, so in this case if i pointed the file to C:\mirc, then i would now have something like..
C:\mIRC
|
|-Themes
| |-Manager.ini
| '-RedTheme.ini
|
|-Protections
| |-ctcp.ini
| |-channel.ini
| '-other.ini
|
'-Bot Commands
|-Query
'-Channel
|-help.ini
|-accesslist.ini
'-modes.ini
Hopefully you can follow the directory tree, but thats the idea. With each Tree dir, is a new dir in the same folder the tree is originating in. From there, you can organize the remotes, and make them easily selected.