Nice work!
I’m off to bed, but will give you a quick bit of info. We have an amazing community here and I’m sure you’l get better help when everyone wakes up 
No, there’s no interface command to align artwork. (There should be though!) If you are talking about a file that has both rastor and vector pieces, you can try saving the aligned file as a PDF and importing int the GUI. The GUI can not process clippaths yet and personally I find PDFs a bit iffy in the GUI sometimes. It is certainly worth trying a PDF first though as you can import the file straight into the interface without having to manually align it.
My typical work flow is to make a master file in my program (Corel). When I’m ready to print it, I save the rastor portions as a PNG with transparency and the cut/score vector pieces as a SVG. I’ve gotten good at alignment and have a few trick I use, so it’s not a real issue for me. Another thing I do when saving my final rastor parts is to combine everything that’s going to be engraved into one last bitmap instead of smaller individual files.
YES! In short, the GUI uses colors to designate different operation in the GUI. If you are familiar with graphics programs, they typically use “layers” to group things together. The GF doesn’t use layers, instead it groups things by colors.
This explains it well.
and here too
You should start by spending time in the “Matrix” tutorial section. It has everything you need to get you started.
and here