redhatcardmaker, are you talking about adding color to dry embossing?
You could use a sponge and dab ink to the top of the embossing. You can also put ink in the embossing folder as well, if that's what you're using. Dye ink should wipe right off the folder after.
If you're talking about heat embossing, you should be stamping with Versamark or pigment ink, which stay wet long enough to hold onto the embossing powder so it can melt. Then hold the heat gun about 5 inches away, keep it moving slightly, and as soon as the powder melts, move to the next area.
There are also embossing markers (like the versamarker). This would be great if you just wanted to add a little bit of embossing to an image. You would stamp with a waterbased dye ink, let it dry, then use your embossing marker to add some embossing ink to certain areas, sprinkle your powder, then heat as above.