I use NewsGator on my pocket pc and wrote a detailed tutorial about it on my blog. Perhaps you'll find it interesting:
Staying Informed with NewsGator Go!
If I recall correctly, Avantgo allowed you to subscribe to a combination of "custom" channels and RSS feeds. You will only be able to set up the RSS feeds in whatever RSS reader you use.
To set up Mobipocket to subscribe to RSS feeds, you'll first need to locate the feed you wish to subscribe to by going to the website and finding the RSS feed button (orange button). Copy the RSS feed address.
Then open up Mobipocket on your computer, select the orange eNews icon in the left hand column, then select the orange Add eNews icon that you see on the top of the screen and select "Add a Feed."
Paste RSS feed address into the space provided, then select the Next button. You'll see a description of the feed you just added, select the Finish button.