Install polymorph.amxx like any other plugin.
Create the folder /addons/amxmodx/configs/polymorph/.
Create MOD initialization files:
File must be in the polymorph folder.
File must begin with a number.
"mapsfile" must be in the polymorph folder. It should contain all the maps that you want to be eligible to be played with the MOD
If a mod comes with a plugins-<modname>.ini file (like Zombie Plague), it must removed.
If you want a plugin running for all mods then place it in plugins.ini. If you want it running for only certain mods, list it in your mod's .ini file in the polymorph folder.