i did this about a year ago. i got a sqhdc3 15" and wanted to use my pos 12" kicker. so i sealed up the kicker box and ran both subs in different boxes and different amp.
it did not sound that good. i had less bass with both.
so i pulled the kicker out and sold it.
you have cancellation issues using 2 different subs/boxes. hell you can have cancellation issues if you run many of the same subs in your car ... if not setup just right.
so do what you like, nobody is going to say do it .
so pick what sub you like and put it in the right box and it will sound better. thats what i did as i had cancellation .