Every time i create a new template, and set its style to "default" when i save it, and check again, it isnt assigned to the product i selected, it is instead assigned to vbulletin.

When i make a new template, and keep its style as "MASTER" then it works, and stays assigned to the product i selected.

But i dont want my new templates being created/stored in the master style, because then they show up on the list in order, instead of under the "Custom Templates"

Am i doing something wrong?

Nope, that's the way it works.

I have seen hacks that add new templates, and they arent added to the master style.

also to prefix a template for later sorting.... do i just prefix_ to the begining of the name.

Like when it asks for template name, I can put prefix_templateX and prefix_templateY and be able to group those according to prefix_ ??

yes you can

New templates for products are designed to be added to the MASTER style, if you want them in some sort of order then you will have to name them carefully.