Fallow the manual, then use the side glass to be sureUm, there is a sight glass on the side of the engine that allows one to 'see' the oil level. There are also hash marks that show the high / low levels.
Overfilling any engine with oil is a bad situation as the oil can hit moving parts and foam up.
If your kinda new at this (or even if your an expert) there is document somewhere on this site, its a shop manual for the bike. A must have for sure. Will answer a lot of your questions.
3.5 qts with a new filter did not even bring mine up to window and I waited over 30 minutes for it to settle.
I just put 4qts in with a new filter and it sits just under full mark where I like it.