Cropping.

First, crop out any black borders of the video by using the null transform filter.

Then select Cropping...

You can use your mouse to drag the edges so that all the black border is gone.

Other filters.

After cropping, you can then apply any additional filters such as colour/brightness correction and denoising. It's reommended to apply colour/brightness correction before denoising. This should be done before resizing.

Upscaling with Super Resolution.

When upscaling with Super Resolution, it's recommended to use several instances of the filter each at 200% till you get to your desired resolution.
For example in order to upscale this DVD from 720x432 to 1920x1080, you should use 2 instances of Super Resolution. First one at 200% to 1440x864, then the second one to exactly 1920x1080

Select video compression to Lagarith Lossless Codec and configure accordingly.

Save the video to avi. You can then compress this avi file to video codecs such as 2-pass x264, which will be much faster from a lossless avi.
You can check out How to encode lossless AVI with x264 using MeGUI.