My pool and spa are at the same level, more or less. When the spa is full enough to spill, it's about 3-4" higher; even with the top of the skimmer actually. Imagine that!
My plumbing has two 3-way valves, one in suction and the other in return. Normally, about 20% of the return runs through the spa, and none of the suction. When I want to use the spa alone, I turn the valves to spa in and spa out. The heater doesn't care what it's heating; I use the pool temperature setting for everything.
I like my setup. When it's time to vacuum, I set the valves to draw from the spa and return to the pool. Then I just brush everything out of the spa and into the spa drain. No need to vacuum. Then I reverse the valves and draw 100% from the skimmer (the vacuum) and return 100% to the spa. That way I have no annoying crosscurrents and ripples. Whatever debris is in the pool stays put until I can vacuum it away. And then I just set it back to pool in, 20% spa/80% pool.