Before the knife is heat treated, and after it has been polished and ground, heat up the section you want to stamp the mark into till it's bright red, then take a stamp and whomp it with a hammer into the steel.
That is, if you have a hardened steel stamp with the logo you want. Acualy, you can do this with cold anealed steel too.
Then when you go to do the final finishing, you polish off any rough corners that have been raised.
I tried a few of these, but decided I like the looks of an unmarked blade better.