dye the deeper areas but not the surface?

[dougfergy]

That is the trade off exactly.  If you use one that is a little more liquid, like Eco-Flo hi-lite stain, it goes on with a dauber and I wipe it immediately with a folded paper towel and it highlights the impressions and stamping nicely.  I also use it as a light stain sometimes.  To me, it seems to be a little more permanent so you want to wipe it off quickly or the color will really set into the leather and darken your staining if you have some.  I like the Briar Brown. 

On the last sheath I made I had stamped the front and stained it with an Oxblood stain, then did a quick wipe on and wipe off with the Eco-Flo and it colored the impressions nicely without darkening the rest very much.  On the back the leather was smooth except for my maker's stamp.  I wiped on the eco-flo and let it set for a couple minutes before wiping it off and it gave the leather a nice color that contrasted with the dark oxblood front and really darkened the maker's stamp to make it pop.  Pick up a few different antiques and hi-lites and do some playing around with them.  I think you will like using them and figure out what works best for you with some trial and error.