Is there a plugin similar to how the blogroll works for an additional way to add external links? ie. I’d like to have two totally different sections in my side bar for links, not just under different categories.
If you use a plugin like exec-php, you can customize your own widgets. Then you could have one widget that pulled up one set of links in a given category (or several categories) and another set of links that pulled up a different set of categories.
And then you need to learn to call certain categories and not others. Information about this is often discussed in connection with The Loop, but much of this applies to the sidebar as well. So you need to learn a bit about template tags: