New bike/fazer owner, proper way to go about the initial service?

[His Dudeness]

It should line up pretty easily. Your end can has taken a bit of a beating from the swing arm so that could be the problem. If you take the bolts holding the can out and rotate the can away from the swing arm and then see where the bracket for the can is lining up. You could try taking out the bolt under the foot peg and see if that makes it easier to line up.