MotionEye addons possible

I have recently purchased a few Raspberry PI's and cameras to monitor my recently built CNC to know when the machine has finished and also to monitor it's progress remotely (can take hours to do some machining operations). I have got the PI's and the MotionEye software up and running wirelessly ( thanks again to the excellent videos posted here) but would like to take it to the next level.

Installing MotionEye is like creating a separate OS that resides on the SD card but it leaves all the other I/O unavailable to use. I would like to add this functionality of operating the PI's I/O to be able to operate relays and also take in contacts to stop or start say the compressor or water pump as an example remotely via the webpage and have joined this forum in the hope someone could point me in the direction of how to achieve this.

I'm new to PI's so not too familiar with their operation just yet but able to follow instructions.