That shouldn't affect the way you create a Stage size in QLab;
When you say E2 do you mean the Barco E2 video switcher? When connected to your Mac what does it say the resolution is in Apple-System Preferences - Displays?
Your output devices will generally have a fixed resolution (unless you change a setting in the projector or LED processor). You can still make a Stage in QLab of your desired aspect ratio. In the Stage Edit page (File-Workspace Settings-Video-Video Outputs tab - Edit button) in QLab set the size you want as described in my previous reply and then you can use the Layout and the Warping tab to adjust the position and size of that image on your output display. It is complex and it is worth reading about it in the manual
it is useful to have a grid display when experimenting; you can turn the grid on and off for each region. Or
on the Stage edit page at the bottom left there is a button for Grid Options which includes Export grid image - you can then use this image file in a video cue; have the computer connected to the display and run the video cue with that grid image and then go to the Edit Stage page and try adjusting to see what the various controls do, until you find something which looks right. If you can't see the screen from the op position having QLab remote on IPad to adjust stage settings make this process much easier. You can also experiment by connecting a second screen to your Mac to get familiar with the controls so when you get in the theatre you know how to achieve what you want.