I just discover how to do it now, my bad.
this provides some help.
Basically i was putting the folder in themes with the same name as the .cfg (ex: custom-test).
To make this work the Collection .cfg in .emulationstation\collections should be custom-NAME
The Theme .emulationstation\themes (create the folder if u didnt have one) copy existing theme that u want to customize from Theme folder in /etc/emulationstation/themes to the new folder that u just created, then the new folder should have the name of the collection "NAME" and not the full .cfg name "custom-NAME".
U can copy the .xml from other collection then just tweak it, it is actually super ez.
Edit: for Automatic collections just do the same process but the names for the folders are "auto-lastplayed", "auto-favorites" and "auto-allgames".