Using the midi controller within Protools allows a lot more flexibility and ease of use, especially to change it after the fact, not only switch out sounds, but velocity, timing, etc.
There are a lot of functions so it can seem intimidating at first, but I think you'll enjoy it once you get used to it.
I don't know of specific video tutorials on drum programming in protools, but you might check out Groove3.com, to see what they have.
I can highly recommend a book that's not very expensive, called "Producing in the Home Studio with Pro tools" by David Franz - 3rd edition:
http://www.amazon.com/Producing-Stud...0779418&sr=8-1
This really helped me with all aspects of protools and there's extensive coverage of working with midi. This book came out before Protools 8, but 95% of it still applies. You can find out the updated midi features or protools 8 through other sources.