The main pool circuit should have returns to both the spa (for the spill over) and the pool. There should be a valve that will let you control how much water is directed to each. You don't want all of the water to be returned through the spill over, you need to be able to control this. If you have such control you can simply set all the water from the main pump to draw from and return to the pool, or just have the main pump shut down during use of the spa.
The spa circuit will similarly be drawing from and retuning to the spa through the jets, which are seperate from the returns used by the main pump. That all works fine and you see that you can seperate the water flows in the two, however if you ever want to heat the water in the pool you need a way to draw pool water into the spa circuit ,which is where the heater is. That heated water is normally returned to the spa via the jets. But, if you are trying to heat the pool that's not very efficient, so you also need a way of returning that water to the pool instead of the spa. So, I have a couple extra valves that connect between the pool and spa circuits on both the suction and return side for heating the pool.
This all makes for a few extra valves but it means I can draw water from pool or spa and return to either pool or spa, and I can do it either with the main pump (which has the filter, solar system and SWG in it's circuit) or with the spa pump (which has a heater in its circuit). I can heat the spa with solar, heat my pool with the spa heater, empty the spa to the pool, etc. lots of options and flexibility.