I will start my first stereoscopic video production. So I am playing around with NEO 3D to see if this is the right solution for me in the editing process. The video I have to shoot is for a double beamer projection in 720p. For the shoot we will use a side-by-side rig with modula-cams. So whats the best for the resolutionsettings of the cameras. Should we use 1080p due to cropping reasons cause we will shot parallel - or should we choose the final resolution for the projection? Or is it possible to crop my 1080p files within NEO 3D to 720p?

Work at 1080 as long as possible. Render to you target resolution. I would recommend the same for 2D.

If I shoot parallel in 1080 and use the convergence settings in NEO3D I have to crop on the left and reight side. So I can use the autozoomfunction but then my pixels are blown up. Cause I need only 720 I thaught I can crop manually to hold the full pixelinformation. Is there a way to do this within NEO3D? Or should I do all my edits within 1080 and create then a cineformmasterfile and convert this down to 720?

Make 1080 master and convert down.