A couple of things:
1) Even though all of your windows may look the same, unless your house is brand new, they’re not – each plywood sheet will have to be custom fit to each window to get a good fit. Many people number their storm shutters clockwise around the house or some similar system to be able to put them up quickly.
2) As far as attaching points, yes, get the bolts or lag screws into the studs! Otherwise it’s a waste of time. Most people who board up leave the attaching points marked in some way, usually with a wooden plug or something similar that can be attached with silicone glue and quickly pried out when the time comes.
3) However you board up, it’s best to keep the boards flush with the windows or the siding, because otherwise the wind can get underneath your storm shutters and pop them off in the wink of an eye.