How to integrate taxonomies into permalinks?

I just installed the custompress plugin and I'm slowly working my way through it. Ultimately, I would like to integrate my custom taxonomies into the permalink structure for the site, but I don't know how to "attach" the taxonomy to the permalink structure.

Right now my permalink structure is sitename.com/%postname% but when a custom taxonomy is in place I would like it to read something like sitename.com/glossary/term -- where "term" is the %postname%.

So where do I begin?