If they are adjacent in the cemetery or with other family in a family plot, link them. Transcribe the stones, and if the wife's stone clearly states "Eleanor. - wife of J W Harris", then that is all you need do.
If the stone is not clear but you know she is the wife, then you can put it in the NOTES as Eleanor - wife of J W Harris.
When I am doing family plots with multiple members, like parents, a child and his/her spouse and other children, and I am certain of the relationships, I put those clearly into the NOTES section. You can also put them in "relationships on the stone" but with multiple stones, it will create ambiguous relationships, so I don't do it in that field set.
I you see or know the marriage date, be sure to include that in the data fields.