Sounds like an interesting project! 
For anything like this, you first need to define the physical changes in the environment that you are going to track. Once you know those, you can figure out what devices you’ll need to track them. So how are you going to tell the difference between actually working at the standing desk and walking across the room near it, for example?
Also, do you use the same desk in a seated position? That is, does it go up and down and you’re trying to track when it’s elevated? Or do you use a different desk when you are seated? The reason I ask that is if it’s a desk that you only use as a standing desk, you could just put a pressure mat in front of it and get the data that way.
If it’s a desk that can go up and down and all that, one of the easiest things might be just to put a motion sensor in a fairly hidden position and just wave your hand in front of it when you want to start tracking. And another similar sensor to track when you stopped. I have a motion sensor on the side of the nightstand next to my bed facing the bed so it never gets triggered accidentally. I just wave a hand over it when I’m getting out of bed to turn on the lights, for example
Or again if the desk lifts up you might be able to just use a contact sensor that will know the difference between desk lowered and desk raised.
You might also find the following thread gives you some additional ideas: