Are you refering to a makers mark or damascus? For a makers mark it seems lots of people use etching machines. There have just recently been some threads about these and if I had bothered how to fully use the posting interface I might be able to give links to them. Since I haven't I can't. For etching the whole blade ferric cloride is common, though pretty much any acid will work. Use it diluted so that the reaction rates of the diffrent metals will be different. As for the depth of the etch, that is dependant on how long you etch it for. Check on it every 10 to 15 minuets.
WS