You can create two different podcasts by creating two different links in the Menu Manager to the Podcast Suite. The parameters on the right will allow you to select a specific section/category to podcast from. This way you can have one feed for the sermons and another for the radio show.

The only issue you're going to run into is that the Manage Clips screen will manage both sermons and radio shows. All of your media will be in one folder, so it might be advantageous to come up with a naming convention so the two don't get mixed up.

Other than that, you can separate the episodes out by using Joomla's section/category system. My church has a "Podcasts" section, with separate categories (and feeds) for audio and video.