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I have tried to check for previous posts on this but have not found any, apologies if I have missed them.

I find it hard to input information using the mouse into a cockpit, say changing the autopilot altitude setting by clicking on the knob, because I find it hard to hold my head steady while doing it, so the mouse moves away from the relevant knob.
Is there a way, say by pressing a key, to lock the track IR position just while the mouse is being used to input information to the cockpit?
Or is there another solution?

Steady. That's it.

There's a Pause setting in TrackIR. Set the hotkey and pause when you're looking at anything in the cockpit.

Going to agree with Jerriko, Pause (default f-9) is great for this.