The spa is still one with the pool water, but with the smaller volume, you only need to replace that water a couple times a day with the bulk chlorinated water from the pool. You would not normally test the spa water only. I suggested it to be sure the FC drop in the spa is not too much with the lessened replacement of that water with the pool water.
Your pump most likely can run at 1500 rpm or so most of the time. In Spillover, I would program it to 2000 rpm or so and try that.