The cyan filter attenuates red light. In a perfect world, with perfect cyan filters, and variable contrast paper that has absolutely no red sensitivity, adjusting the cyan filter would have no effect on exposure.
We don't live in a perfect world.
So I recommend using all three filters, even though the cyan filter should have very little effect.
For panchromatic materials, you need to add equal amounts of magenta, cyan and yellow filtration to reduce exposure.
For non-panchromatic materials, that have no red sensitivity, the effect of adjusting the cyan filter should be very small.
By the way, we are assuming here that the settings on your magenta and yellow (and cyan) filter dials accurately adjust the amount of magenta and yellow (and cyan) filtration in a linear way. If they don't, making equal changes will have an effect on contrast as well.