You can track as many layers as you like in a mocha project concurrently, but you can only export them one at a time, as you need to select each layer back in AE to apply the separate data to.
Every layer you draw is a new tracking layer. If it’s cog is on in the layer controls, it will track. If you draw three layers in mocha and track, it will track them all at once.
You can then select each one individually and export the tracks back to AE.