You will need your folders set up in this order:
"Base/Models/Players"
Inside the "Players" folder you will need the JK3 "_humanoid" folder, then ensure the model you're loading has been imported into the "Players" folder, with a "model.glm" and "model_default.skin" inside your folder. From the Blender menu click to import - JA Ghoul 2 model:
Then select your model's folder choosing the .GLM file, but before you click to import, ensure you have filled in the base path on the right of the window that pops up to link with the location of your base folder. For example, mine will be filled in as "d:/jka/base". This will always be left blank, and you will have to fill it in manually each time. This goes the same for exporting JA Ghoul 2 models.