2 switches, 2 circuits, same box
I mix multiple circuits in the same box a lot. 

I would color the wires for the second circuit differently.  

Use gray shrinkwrap or tape on the second circuit's neutrals.   Then use brown or blue shrinkwrap or tape on the second circuit's hots.  

If the next guy is dumb enough to mix gray neutrals with white neutrals, well, you can do what you can do, but you  can't fix stupid.  

I for one prefer to also use a differnt color for switched-hot (typically red), so mark the switched-hot for circuit 2 with both brown and red.