I agree with Juan. It is more challenging to perform the single legged drills when the other leg is unclipped. You can rest it on the back of your trainer or ideally keep it raised above your trainer behind you. That said, be sure that you engage your core this will help prevent you from leaning into the working leg or compensating. Once you start losing the even pedal stroke and you feel the push and pull fall back into your rotation, please end the drill. If you continue to push down, pull up when you are fatigued, you are only ingraining poor form.
In addition, keep the cadence relatively low for single legged drills. At a higher cadence, it’s harder to maintain good form, engage your core and it increases your likeliness of compensating. Finally, if you have any type of injury particularly with your back, please do not do single legged drills. This would be a great time to do single legged drills when both feet are still clipped in. This won’t provoke compensation that could worsen an injury.
Great question! Good form is the foundation of injury free, powerful cycling!