You can use your everyday bikes on the trainer. I've heard of one single carbon bicycle frame that broke on a trainer. It's almost unheard of. But a towel over the stem and front brake will go a long way in preventing rust in those areas.

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Madison photographer Timothy Hughes | Instagram

I am pretty sure you will each need your own TR plan, because it indexes everything off FTP, and I do not think it has provision for multiple user profiles. Plus, you may be working different plans, and it has a one-plan-at-a-time model.

As far as which bike, I would not worry about bike damage. But, for the sake of simplicity, I would leave the common bike on, if it fits you both, for the base building plans. However, when you get closer to a race and into specialization, then I would swap to individual bikes to get comfortable in your respective positions.

Two subscriptions.

Better to swap the bike that you ride on the road onto the trainer. That's what makes the a trainer better than a spin bike. It's your bike, your fit, your comfort.

You might want to look into PerfPro Studios. It is ~$100 one-time fee and allows 3 riders to ride simultaneously. You can use your kickr + an old magnetic trainer, rollers, etc. Obvoiusly only the Kickr will get the power transmitting unless you have an on-bike PM. Alternatively you can ride 1 at a time and easily switch the rider profile. To me this makes much more sense than paying ~$20 a month for TR/Zwift/Etc.

To be clear, Perfpro has a very large library of workouts, however it does NOT have any workout plans. That might be a deal breaker for you, but if you are wanting to save bucks PerfPro (or even goldencheetah which is free) will save you money in the long haul. Reading books like Joe Friel's Triathlete and/or Cycling bibles will help you learn how to formulate a training plan and follow it. I know my local library has both of these books available and if your library doesn't then you might be able to ask some people you ride with if they have a copy.

There are other advantages to TR, such as in-cloud data but for me personally I am riding near my PC/laptop to use Perf-Pro and the few times of the year when I am not, I am able to use my phone to control the kickr and complete my workout.

Any bike will be fine on the trainer, but I wouldn't use race wheels while riding a stationary trainer. Definitely recommend a rag/towel covering the stem. You will want large fans blowing air on you since you sweat a lot more indoors than outdoors without the wind. If you don't use a rag/towel to cover the stem then your sweat can corrode the bolts. Last year I had a teammate who had his stem fall off while riding a club ride and it was because of sweat and not covering his stem.

Sounds like you need a second Kickr.