By now all that should need doing is to make sure that you have the various models eg.

playermodel.md2 - NEEDS TO BE CALLED TRIS.MD2! weapon.md2

The skins eg.

playermodel.pcx weapon.pcx

And finally an icon for your player/model/skin eg.

playermodel_i.pcx

As far as directories go they all need to be in the Quake2\Baseq2\Players directory in a folder under the name you want the model to be known as eg.

Quake2\Baseq2\Players\Playermodel

Providing all this is in order you should be ready to begin.

GOOD LUCK