Confused by Smart Trainer Options

If your workouts have power zone targets that is what the watch is using to determine where to set the resistance. I believe it's using ERG mode and will automatically adjust the resistance to keep you in the target power zone for the interval.

This is really frustrating.  The watch takes control of the trainer when on Zwift.  Zwift should control the trainer in this instance.  It's all well and good being in ERG mode, but this makes Zwift boring as the ascent and descent functions don't work.  It's just like being on a 'dumb' trainer.  Even stranger is that Garmin owns Tacx (my trainer is a Tacx Vortex).  Please could someone let us know how to get rid of the options for indoor bike, or which setting to use to just get the watch to record and not control.

If you don't want the watch to take control but still want to record data from the trainer do not connect it as a smart trainer to your watch. Instead connect it as a power meter and/or a speed and cadence sensor. If you connect your watch as a smart trainer along with Zwift they conflict as to which should control and the trainer has no way of knowing which should so it seems to pick your watch. Disabling the smart trainer connection before connecting Zwift should fix that.

I might do something different but it does work for me.

Zwift is connected, it controls the trainer. Edge and the watch are also connected as a Smart Trainer, I choose Free Ride on both and it works fine for me.

Same for me. Using zwift with Garmin (paired as smart Trainer) and zwift is controlling as it should while in free ride mode

When I enter free ride mode on the watch, I hear the resistance changing automatically. Then I start my workout in elite myetraining app, and then the elite app controls the resistance as normal. This is acceptable for me. (Strange, but IF you have a garmin, then anything can happen, you know)

This is my workflow for Zwift on AppleTV, my Garmin and my Wahoo Kickr:

1. Open Zwift and pair the Kickr and Garmin HRM Pro Strap via Bluetooth.
2. Select Sensors on the watch: HRM-Pro via ANT+ and the Kickr as a power meter only (power and cadence are transmitted on a single channel with the Kickr). Do not connect as a Smart Trainer. 
3. Start the indoor bike activity. When it suggests “Free Ride, workouts” etc, press the back button once which will take you directly to the activity screen where you can start the activity as usual.
4. Start Zwift. This will allow Zwift to control the trainer directly and the watch just records power, cadence and HR.

I then have the watch sync to Garmin Connect which records my training effect and training loads.

Zwift is set to sync with Strava.

Be aware, that the distances travelled on the watch will be different to that reported by Zwift but that is OK. Training load and effect are not effected. The watch has no idea of the virtual world that you are riding in so cannot see elevation changes, only power and cadence changes.

Zwift understands the virtual elevation changes and can change your reported speed when the elevation changes.

Think about it as Garmin recording your ride on a flat track where power changes directly effect speed...the more power, the faster you go. If you have calibrated your wheel size when you selected the power meter, this will be equivalent to you riding your own Bike on a flat surface (I use 2335mm as the diameter of my 29” wheels).

With Zwift, more power with zero elevation change has the same speed increase as Garmin. With elevation changes however, the increase in power doesn’t necessarily translate into extra speed therefore the recorded distances will be slightly different.

The outcome is Zwift and Strava report the speed and distance from the virtual world and Garmin captures what it would have been if I rode my own bike on a flat track. Training effect and training load would be identical between both scenarios.

I did what TheOtherPhil said and it worked fine, but the problem is that it counts me as doing 2 rides (one Zwift ride an one indoor bike) instead of 1, so my weekly distance stats are doubled. If i delete the non-zwift entry, then all my training stats go away. How do I get the watch to recognize that the Zwift ride and the "Indoor bike" are one and the same, not 2 separate workouts? 

how are you getting speed and distance to record via garmin using this pairing method? when i connect the smart bike as power meter only, speed and distance are recorded as 0 via garmin

You can't get Garmin Connect to combine the two rides but there is sort of a workaround. Record the workout on both Zwift and your Fenix 6. At the end allow the Zwift workout to sync to Garmin Connect and discard the workout on the Fenix. If you check the widgets on your Fenix after doing so you'll see that things like recovery time, training status, VO2 max, training load, etc are still updated. You do lose the training effect stats that are reported at the end of the ride if you save it but as far as I can tell this method preserves the important stats. The ride distance from the Zwift workout will also sync back to your Fenix via TrueUp.

This is the method I use since I want the recovery and other metrics to update but I want the distance in Gamin Connect to reflect Zwift.