Actually, as far as pain goes, my hand hurts a lot sooner with a mouse than with my laptop's touchpad. The touchpad makes it easier to (1) switch between the right and left hands to move the pointer around and (2) move the pointer around without moving my wrists from the keyboard, and both these things really improve computer usage long term for me.

I haven't used a mouse in years.

I actually work faster using a [touchpad + keyboard] vs [mouse + keyboard]. The trick is placement. The touchpad needs to be right below the keyboard (like a macbook layout) so you can switch faster between typing and moving the cursor as opposed to using a mouse. If your OS / trackpad supports gestures, that increases speed of use as well.

For comfort, imo the whole thing needs to be lower, closer to your legs. If you're using a standing position instead of sitting, just change the position to closer to your thighs.