I don't know about the Magazine template, and I only used one size of icons, not large/small, but here's how I got going with Category Icons and Suffusion. Actually, I had to switch to Category Icons Lite, but I am very pleased with it, because it was much easier to implement -- I struggled for days with Category Icons itself.
Here's the discussion I had with the developer of Category Icons Lite:http://wordpress.org/support/topic/plug ... -suffusion
Anyway, one icon -- maybe the small one? -- appears in front of the category name in the category list -- for me, it's in the sidebar. (I also modified the CSS for that unordered list, to get rid of the bullets.) The other icon -- the large icon, I imagine -- appears in front of the post title. I was expecting it to be under the title, where the category itself is listed, but that's not what happened. Note that you have to make some modifications to a couple of files to get the icons to appear with the title -- see the above link for info.
You can look here to see how I implemented the icons:http://www.foryourwordification.com/
(still under construction!)