Just follow the instructions. I don't know about your bike, but one of the bolt holes on my Yamaha is not a blind hole (blind holes don't go all of the way through, they're the easiest). It goes through to an oil passage. Are any of the bolts significantly longer than others on the cover? It would be difficult to flush chips out of this passage with the cover installed which is why I suggest removing the cover. The passage on my Yamaha is also after the oil filter so any chips left in it will go through the engine. It usually involves draining the transmission oil, draining the coolant, removing the water pump cover, removing the brake pedal, and then a bunch of bolts. During installation, you'll need to rotate the water pump impeller so it lines up with the gear on the crank as you install the cover which is why you remove that cover. A new side cover gasket is inexpensive.