I took everything apart that I could (the nut, bridge assembly, and the brass block under the bridge). Other than being tedious to do, once they were off the body it was pretty straightforward to disassemble and polish. The frets and tuning machines were also pretty easy - you just have to be very careful if you have a wood finger/pegboard (mine has a phenolic fb and a walnut pb). Now the logo was a little trickier. I took alot of time and used VERY LITTLE polish (it doesn't take much). Just lightly dabbed it on with my finger then buffed it off (again, carefully).
I used Flitz polish since it was the one recommended by Alembic. You can get a tube of it at Ace Hardware for $9.49.