There was a small black "cap" included in my install packet that looks like it is meant to go into whichever hole you drill out for the conduit entrance that would provide a tight fit for standard 3/4" liquidtight flex....however I didn't notice it until after my electrician had already run the conduit in so I haven't used it. I suppose i could snip one end to fit it over the conduit. Or you could just use a bit of expanding foam or silicone. I wouldn't bother sealing the other 2 unused entrances inside the equipment compartment as there's really no access to them from outside assuming your tub is on a continuous flat surface.
