There is a permanent probe mounted in the box and connected to the PID that is used to measure and indirectly maintain the box/cook temperature. There are two external probes that you can connect/disconnect on the back of the PID that are for measuring food temp. The 1st food temp probe you can program against. The 2nd food probe is for measurement/reporting only.
For instance, when I do a turkey I use both food probes and stick one in each breast. I program the smoker to turn off when the 1st probe hits a specified temperature. (Blanking on the temp at the moment... 170?) I just use the 2nd probe as a sanity check.