Hi,
The difference is the base voltage needed to turn on the transistor? xV above 0V for NPN and xV below V+ for PNP.
It sounds like maybe you will use a BJT as a switch, so whether you use NPN or PNP ...the relay? sensor? will not be powered until the MCU turns on the BJT.
Do you mean a sensor will go into the MCU, and the output of the MCU will go into a BJT which will control a relay?
You should post a schematic of the circuit, otherwise it's just guessing what you are concerned about.