I'm having real trouble getting the 3d models to act correctly in terms of collision, i believe tis is done thorough the scale option? How do you get the entities collision to match the 3d Model? I can either walk right through my model or the collision is off and am able to walk over it.

You can't walk through any models, they're making a box collision that occupies the whole model area. So if you wanted to make some kind of ladder or passage, then, tough luck.