Here is my system:
I bought a cheap but durable duffle bag from Target; as well as one of those car fender protection mats like Jiffy Lube uses. (Available at Wal-Mart.) I keep my medium size Box Anchor in there; wrapped in the mat. I take the entire bag (handy dandy and safe shoulder strap) up to the bow and pull out the entire mat and lay the mat down, and spread it on the bow when throwing anchor. (I also do this on the sunpad, drop the anchor over the side, and back into position, then go up to tie off). It is at least 1/4 inch thick of dense padding. It allows me to set the anchor on the bow, with no risk of chipping the gel. I keep the whole thing under my backseat, where I used that garage floor interlocking material to create bit of a storage section just for the anchor, so as to not go places I shouldn't. It works sweet, and some think it is overkill, but I don't mind at all.