Mark I prefer to stencil before deep etching. The way I do it is when the blade is finished I will flash etch in feric cloride (give it about a 30 second to one minute etch), pull it out, clean off w/ a baking soda solution. Then I etch the logo in it. Now what you have is your etch w/ a faint damascus pattern showing in the background. Now reclean everything, mask the logo etch w/ fingernail polish. Go back to the ferric cloride and put the final etch to the blade. After etching remove the finger nail polish w/ acetone. Try it on a piece of scrap damascus to see how you like it.
If you wait until after the deep blade etch to put the logo on it tends to get lost in the damascus pattern.