I just put on running boards on my 2011 x5 a couple of weeks ago and the type of rivets used in the wheel wells are called POM rivets. They cannot be reused and to remove them just push the pin in first then pry them out. You can get the exact same rivets from the dealership. I used this POM riveter from Harbor Freight with the BMW rivets and it worked perfect:
http://www.harborfreight.com/hand-ri...ets-97757.html
As far as sealant goes the older instructions show using window caulk and the newer instructions do not. The bolts that came with my kit seemed to have some sort of blue sealant under the head of the bolt but I went ahead and put window caulk in the bolt holes. Better safe than sorry and it couldn't hurt.
Also the rivets on the bottom of each side that sort of look like screws have to be pried out. To do that I used one of these:
http://www.oreillyauto.com/site/c/de...1693&ppt=C0063
I ground down the blade on it to make it a little thinner and easier to get under those rivets.
Also I didn't have to remove any rivets in the front wheel well, just the ones in the rear wheel well specified in the instructions.