I use the Cuttlebug embossing folders. Take pigment ink (because it takes longer to dry), and ink the folder. If you want the embossed/raised pattern to be inked, ink only that side being careful not to get the ink in the non-raised parts of the design. If you want the background to be inked, ink the other side of the folder that has the indents (but don't get ink into the indents of the pattern).
Then place your paper in the folder and run it through the machine. You'll then have either an inked embossed pattern or a background (negative space) that is inked.
Go to my gallery and check out the dark blue "M" letter. I used navy blue cardstock and inked the background (negative space) of the embossing folder with gold pigment ink. This resulted in navy blue raised flowers with a gold accented background.
The folder is easily cleaned with your favorite stamp cleaner.
Feel free to msg me if you have any questions about this technique.