make sure it's mounted properly. I had an RDS that was slightly out until I realized that it was just slightly out of alignment on the rail. Snug up the mounting screws and check that it's flush on both sides and lays flat.
are you calibrating indoors? it will be pointless come an outdoor event with winds. I generally set mine to center and adjust from there once I hit the field. what distance are you spotting at? don't know what RDS you are using but pretty much keep turning the screws until you get the dot to where you want it. you may have to mentally adjust one way or the other if you cannot get it all the way to where your BB's are hitting.
You can get a lens protector but if it's a cheap RDS, I use them as a disposable item. I have yet to see one break in a game but I have seen one or two broken ones but unsure of how they broke.