Technique
Set the camera to the fastest frame rate possible, then conform the footage within Final Cut so the frames map 1:1 before applying Twixtor.
For Example:
Camera at 48 fps
FCP Project at 24 fps
Drop the clip onto the timeline, select it, then choose Modify→Retime→Conform Speed from the menu bar. The clip should now be slowed down to match the frame rate of the project (i.e. a 48fps clip in a 24fps project will play at 50% speed, and no frames will be dropped).
Twixtor creates smoother slow motion when Optical Flow is selected as Final Cut's Rate Conform setting like this:
Apply the Twixtor plugin to the conformed clip.
The two settings that smooth out slow motion in Twixtor are Frame Interp: Motion Weighted Blend, and Smart Blend like this:
Example Footage
An example of footage that uses this technique is displayed below. The best footage for use with Twixtor has a clearly defined subject in motion against an immobile background with few details. The footage shown here breaks these rules and is included to display the undesirable artifacts that may occur. However, Twixtor still does a decent enough job and it is not unwatchable.