The easiest thing is just to switch cassettes, put the nine speed cassette on the PowerTap wheel. Remember to remove the 10 speed shim from the PT wheel before you put the nine-speed cassette on. You'll need a chain whip and a cassette ring removal tool (a wrench) and a few minutes, that's it. The ten speed spacing on the cassette, between sprockets, is narrower than that of the nine-speed obviously and so your wider nine speed chain will not ride/shift well on the 10 speed cassette.
Swapping cogsets each time I want to use the trainer is not a viable solution for me. Too much work, especially considering I'd be doing it every week.
But, I think I found an answer, another PowerTap! I decided to get a used PowerTap wheel to use on my indoor trainer. After some searching, I found one on Ebay. The price was right and it will allow me to have an extra wheel if I need it. The PowerTap is a few years old but works fine. It should be a perfect solution, allowing me to keep my old 9-speed setup to use on the trainer and outside if needed.