Not sure exactly what you are after here. Are you proposing a pool/spa combination or separate equipment? Typically a spillover spa has combo equip so the pool and spa are at the same temp except when you turn the spa on to heat, at which time the spillover effect stops.
Usually a separate system does not include a spillover spa although the effect can be achieved through other means. A separate system will allow you to keep the pool and spa at different temperatures all the time. I'm sure I haven't answered your question but I'm really not sure what you are looking for.
Proper sanitizing and circulation should minimize algae growth in any pool.

Thanks for replying... I probably was not clear in my original post. Here are the facts as I know them:
- we will have only one pump to be shared between pool and spa
- we will have a spa with spillover into the pool
- when we heat the pool, we want to heat only the pool and not the spa. Also, the pool will have a cover on it (for up to 6 days straight)
- when we heat the pool, and only the pool, the spa cannot spillover into the pool (too much heat loss when the hot spa water contacts the air)

So the questions are:
1. how do I heat the just the pool while still circulating/filtering the spa water?
2. for those with pool/spa combinations, how do you heat the pool withpout heating the spa?
3. if I need separate system to accomplish what I am after, does that mean I need 2 pumps and 2 filters?
-Gorilla

Ok. With a conventional single circ pump or combo system the pool and spa are at the same temperature except when you heat the spa, then you stop circulating the poo and your spillover stops.
In order to heat the pool and not the spa you would have to stop returning pool water through the spa and your spillover effect would stop.
In order to heat the 2 bodies of water to different temperatures you would need 2 circulation systems and in situations like this there is typically no spillover effect. The pool and spa are considered 2 separate bodies of water. I have dealt with this situation many times by installing a sheer descent in the pool circ system between the spa and pool creating the illusion of a spillover.
Hope this helps.
How far is the water falling that you are so concerned about heat loss?

Cascade: Thanks for the additional ifo. That was very helpful. Now I have the guidance to make an intelligent decision.

As for the spillover water, it would fall 12"... but from what I've read about returning heated water back to the pool, the heated water should reenter the pool as far below the surface as possible.

I would not ordinarilly be so concerned with heat loss if I had planned to build a smaller pool like my last pool (11,000 gal)... but with a proposed volume of 27,540 gallons, the heating system needs to be efficient as possible.

-G