Can I use a capacitor instead of battery?

Capacitors are worse than useless for your requirements.

 

However I’m not sure if you have an idea if three batteries and redirection is the best idea or if it would even work.

“Challenge your assumptions”! I mean to ask yourself the question, what is the minimum and maximum number of features that I need. Do I need multiple batteries and if so, how many? Do I have to redirect charging, but can my design be realized without that feature? Where can the design fail and what are the effects of that failure? Do I need extra circuitry to ameliorate that failure?

Challenging assumptions are necessary for the best design. It is how you simplify the design, minimize power requirements, minimize size and weight, etc... Its how you find a final solution that is cost-effective, reliable and functional.