Just keep in mind that modern biomedia such as sintered glass has orders of magnitude more surface area for beneficial bacteria. Scrubbies are great in large a w/d. IMO they have no place in a canister where space is limited and you need to make the best of it.
Whenever I set up a new FX5 I always fill the first tray with scrubbies from the submerged section of one of my wet/drys and the other two trays with Substrate Pro in media bags just to help seed it quickly. After a month I switch the scrubbies out on the first filter cleaning. Works great but I've never used them long term or in all three trays.
EDIT: "instead of the foam", you mean for mechanical? I think the holes in the scrubbies are too large for mechanical.