[Sharc]

I don't know what a MAGIX pen is an what it does. Is it a capture HW/SW package with an on-the-fly encoder?
First of all you should capture your VHS tapes lossless using HUFFYUV, Lagarith or UTVideo codec. Composite video is not the best choice as it is prone to producing dotcrawl and rainbows, but I understand you have no other choice.
Once you have succeeded with the lossless capture (no dropped frames, etc) you can view the captured video and only then decide on next steps like cropping, denoising, deinterlacing/bobbing. You have to do some test encodes using x264 (AVC) or x265 (HEVC) and see what CRF or bitrate gives the desired quality level. Finally, one needs to mux video and audio in a container format of your choice.
The first step is very crucial though. If the VHS capture is flawed it is nearly impossible to recover any losses at a later stage.