If your pool and spa water are co-mingled in the filter, pumps, etc, I am not sure how you would separately heat the spa water. If you have separate loops for each, then I would expect separate heaters for each. I am guessing you are asking for a future project, so I would make sure this is discussed in the planning stage. We have a separate spa above ground, with the built-in heater. It easily heats the 500 gallons of water and keeps it nice and warm the very good insulation.
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Pennsylvania, for 60+ years, most recently, Allentown, now TV. 
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