For most stained negatives you need to set a color densitometer to the blue channel, or use a blue filter on a B&W densitometer. You have to think like your printing paper when measuring densities. There is less silver density in stained negatives than normal negatives, but there is also stain density. If you use a regular white light densitometer it will therefore read less density than your paper will "see" (ie the negative will print with more contrast than you expect). The printing paper sees both the silver density and the stain density as additive. This is why a properly processed Pyro negative looks relatively thin and low contrast to the eye, but will print with higher contrast. It takes some getting used to.
The densitometer stuff can get more complicated unfortunately depending on whether you use graded or VC paper, and also depending on what kind of staining developer you use since different developers can produce different color stains. They can range from greenish brown to yellow-orange.