Yes - black is just fine. I'm not sure what model (or even what piece of equipment) you're referring to. Google was no help. Perhaps a picture would help? Edit: a little more Google-fu led me to thinking that what you're talking about is a thermometer. Thermometer =/= Thermostat
The thermostat probe goes between the glass and the heat pad on the outside of the enclosure. The heat pad plugs into the thermostat and the thermostat plugs into the wall. You set the thermostat to the temperature you want your heat pad to reach and it does its thing.
The thermometer is a completely separate piece of equipment. You place its probe right above the heat mat inside the enclosure and it will tell you the hottest temperature that your BP will have access to. If this reading is above or below where you would like it, you adjust the thermostat's setting as appropriate to reach the temperature you would like.
Here's a picture:
Does that make sense?