I wrote this up and believe it is correct, but I could be wrong about some of this:
Code:
quake\joequake // where joequake files reside
quake\joequake\env // custom skyboxes
quake\joequake\lits // custom lighting
quake\joequake\textures // general textures (any map, water, lava, ..)
quake\joequake\textures\bmodels // basic models (health, ammo, etc.)
quake\joequake\textures\charsets // custom character sets
quake\joequake\textures\models // models for models and items (backpacks)
quake\joequake\textures\particles // smoke, rocket trails, etc.
quake\joequake\textures\wad // hud elements (aka statusbar)
quake\joequake\textures\(map name) // custom textures for a particular map
quake\joequake\textures\dm6 // example of a particular map
So, you would put them in joequake\textures\models
If it is an actual .mdl model, it needs to go in joequake\progs
Someone correct me if I am wrong.