Hey Brian, I used 2 or three quick shots of sanding sealler on the faux binding, Then taped it off once it was dry. I found that the stain caused the tape to release in a few spots resulting in some color geting on the binding. Luckly the sealler worked perfectly and the color was simply sitting on top of it, it could actually just be wiped of while it was wet. Once eveything dried, a quick pass with 150grit on a small sanding block cleaned it all up really nicely. I would say tape off the binding to minimize clean up but for the most part the sealer is responsible for the clean edge.
Another way to do this would be to dye then come in with the router afterward and cut the bevel. That is what I did with the headstock.
As for the logo, I think I going to test out this inlace stuff ScottR had recomended to me for another build. Ill try it on a test piece first and hopefully I can just carve out the logo and fill it with this stuff.
http://www.inlaceonline.com/text/products/kits.html