I agree that you won't want the window and the bee entrance on the same side. My window is on the opposite side of the entrance holes. The holes help to illuminate the other side of the hive when I open the window so I'm fairly happy with that. My kit happened to have 3 predrilled holes evenly spaced along the long side. For the first year, with a small population, I only opened one hole. This spring I opened the middle hole so they have and use 2 entrances. (brood nest is still in the front where it started). And just this month, I opened the third hole, but only for ventilation. Yesterday the high was 95 degrees and the bees were hanging out all 3 entrances.
I do have a second hive with a periscope top entrance on one of the short ends, because I was trying what Michael Bush recommends (and I have supered that TBH). That hive has been fun to work with the observation window on the front (easier for me to get to) and the bees on the side don't bump me too much. I have noticed (only because I have a window to watch), that the mortuary bees seem to struggle to haul out the dead bees to the top entrance. The bee has to take multiple trips up the side before finally gaining the top and I frequently find expired bees stashed behind the follower board in the un-used area of that hive.