Tried the opacity trick and it worked pretty well.
I'm new with NCH VideoPad, som I didn't know a way to increase contrast over the two channels in one project. But with a second project importing the first composit and increasing contrast (with a combo of exposure and sharpness)I solved that satisfyingly. Some quality loss as a second gen export ofcourse, but OK.
But I was a bit confused with how the input frames are supposed to look to composit 3d-video?
I usually render two separate cams full res for stereo. But it seems like I will have to combine them to one image above or side by side before I can take them to VideoPad to 3d-treat them.
In that case I might as well use PS-macros to mix down the channels and 3dsMax Videopost to combine them as I have done in the old days.