Not really sure where it’d fit in but I’d suggest getting some outdoor rides in with it so that it’s less abstract. It shouldn’t take too many rides to get a general idea of what you’ll get for different wattages.
Smoothing is a matter of preference to some degree. I use 3 second for TR (though I swear it’s less smooth than my garmin which is also 3s). If it’s too jumpy you’re not missing anything by switching it to 5. The powermeter should be able to sync to any number of devices. They’d see essentially the same data though.
Definitely make sure you’ve got the crank length set correctly for your pedals in the Assioma app and the same for your wahoo. Enjoy, I’ve been using the Duos for going on 2 years and have had a great experience with them.
You can pair eg your head unit with the pedals, and your phone with the trainer, and then run TR from your phone. That allows you to collect the power data separately, and is useful to see how much of an offset is between the two. You’ll only need to do that once or so, to see the difference.
If there is an offset, the easiest way is to activate powermatch in TR, and to pair the pedals as the power source. If there isn’t an offset, it doesn’t matter that much, you could either run the trainer as before, or use powermatch.
Does TrainerRoad record Right/Left data? I don’t think so, but maybe I’m wrong.
My only reliable source of power is the powermeter, so it probably wouldn’t make much sense to compare it to a dumb trainer that I already know not being very reliable.
Outside of simply doing a zero offset and ensuring your crank length is set correctly, don’t do anything else. Just ride as normal and casually pay attention to your power numbers. As you noted, 3-seconds is erratic. I use 3-second as my instant power, and then 10 and 30-second averaged power for my ‘what am I roughly currently doing’.
Look at how things feel in different conditions, at different intensities, and different cadences, and based on different days of the week with fatigue. Simply put: Just passively collect data for a while.
Ultimately, you want to build up a bit of a mental correlation between how these powers feel, and what the numbers show. So that eventually you get to the point where mentally you look at your power and go ‘Oh, right, I can’t sustain 350w for the next 3 hours of this ride, maybe I should chill out a bit’.