You will have a mullion cap between the windows that will cover whichever way you do it. Check the entire opening for level, if it's close start with the window at the highest end, (1) level it nail the bottom then plumb and nail top & sides, then install the next using the level to align and nail the first corner of the second one, then level & nail the bottom. (2) repeat step 1 for each window. If it is too much out of level you may have to; relevel the sills, use a long straight edge to align all 2 or 3 windows a level as possible, from the high end, step each one down as little as possible, or worst case install slightly out of level but square. They should look relative to the ones you take out. If a house is way out of level most people might see the windows do not match the house if they are level. If your friends come over with a level to check if your windows are level, I wouldn't invite them back. Even worse is if you wallpaper with a patterned paper, it will show if the windows don't align with the house. You can choose whichever way you like, it's your house.