John,
 
After inking tissue for margins, use a mixture of 1 part glacial acetic acid: 5 parts 10% NB formalin: 15 parts distilled water.  Let it sit for a minute then blot with tissue and place in your preferred fixative.  The dye will not run or muddy up your solutions in the tissue processor.
 
Hope this helps,
Jennifer Johnson, HTL (ASCP)
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