Oh, sorry, I missed this part of your message.
Unfortunately, the cycle editor is really not usable, I think it is best to forget that it exists. It is extremely buggy, and requires a good understanding of the data structure presented in
this paper. Personally, I only use the cycle editor as a visualization tool.
At the moment, if you need to create complex inbetween faces, the only way I recommend is to understand the data-structure, and edit the *.vec file by hand, which is very technical, tedious, and time-consuming. This is how I created most of the examples in
this video.
Being able to create complex inbetween faces in a more intuitive way is one of the reason why I am now rewriting VPaint from scratch, to become
VGC Animation. Hopefully, in about 2 years, I should have a beta version of VGC Animation in which complex inbetween faces can be created easily. Thank you for your patience!