A general user guide? PTC doesn't have those. There's the somewhat cryptic help files, which are useful if you remember exactly what you are looking for; some special tutorials and that's about it.
Here's a thread on learning Creo http://communities.ptc.com/thread/44546 and http://communities.ptc.com/thread/39315
I went through a bunch of the PTC/University courses, which were uneven in coverage, and lost a lot of time in their course introductions I recall, repeating the name of the course, the instructor, what would be covered (It's a video, provide a written synopsis) and then they spent most of the time with Click this, check that without explaining why any of those choices mattered. Like if the sketch came to 6.012 on a dimension, the instructor wasted time telling the student to change it to 6.00 then click OK.
One area of documentation that PTC should have is the narrative about what portions of it's interface are intended to accomplish and what side-effects/interactions/prerequisites there are to accomplishing those results.
As to your layer problem - hiding parts in an assembly can only happen at the assembly level. A common error is to try to hide a solid feature at the part level, which can't happen. They can be simplified away or suppresed, but not hidden. This would have been explained in narrative about layers and be part of the non-existent user guide.
