It does take quite a while to get used to it, but hopefully he won't need it for long. Unfortunately, at the current time, due to side effects from the radiation and subsequent remedial procedures, I am totally dependent on a PEG tube (and have been for over two years now), but I have one of the low-profile button types, which is the difference between night and day.
When water won't go in, likely the tube is clogged with something. If you don't have a clear tube, it is hard to tell. It's a good thing that you were able to use the plunger to get the "clog" cleared. Just make sure to flush with plenty of water whenever using the tube and get everything either liquid or dissolve your pills in water. The only things that will not work on are meds clearly marked "Do not crush" or time-released meds. You can even take capsules and open the contents and dissolve in water (for most meds).
As others have mentioned, it's important to keep the tube secured. Paper tape marked for sensitive skin worked fine for me, but I rubbed the area with alcohol before applying so that it would adhere better. If you let the tube dangle around, it will pull at your skin. The most important thing is to keep the area dry. I use a square of tissue and change it frequently throughout the day. I also use Neosporin with pain reliever and that has helped a lot with the pain of granulation tissue.
Any other questions, please feel free to ask, as it is a really difficult experience, takes a lot of getting used to, and there is not a lot of information out there. Also, check out oley.org. It has a lot of information about tube-feeding and is helpful.