I am in the middle of this project myself, not on a malibu, but it should be similar nonetheless.
I removed the original kickpanel all together. Because the floor in the locker is not flat at that point, I created a false floor with starboard lite. Then I made a box to fit a 12W7 (about 1.2 cu ft.) out of 3/4" high density starboard. First I will install the enclosure to my new false floor, then I will install the sub (since the enclosure mounts to the floor from the inside), and lastly I am making a "grille" or trim panel that will completely conceal the sub but have a custom, OEM looking, patterned cutout to make it acoustically transparent. I haven't decided whether to do this out of aluminum or starboard.
I'll post some pics when the entire install is complete.