I must admit I struggled at the start, but I'm definitely feeling more at ease with it now, I've probably produced around 40-50 drawings with it and every one feels a little bit more natural. I can't imagine how you managed with a mouse for so long though, presumably you're finding it far easier with a pen?
At the moment I'm only using Adobe Illustrator, so all of my work is vector drawn. I am using layers too but haven't experienced any of the problems that you're having, but I'd imagine that's down to the software. In a few months time I might start experimenting with Photoshop as the brushes seem a lot more realistic, but for now I am going to concentrate on building my portfolio and develop my style a little more.
I know you've seen a few of my uploads, but I'll post one here as requested. This one has just been approved. :)