I am not sure how the "stock" RSM 130D comes, but almost everyone on here has upgraded to Stevie T's Media Basket and did away will all the media that comes stock with the RSM.
If you stay stock (and it seems like your cycle is done), try to see if you can incorporate CPE and Pruigen. The CPE will take the place of the carbon. Both just need to be in the water column pulled by your circulation pump.
As for the rubble? I did that in my AquaPod 12. I'm not really a fan. The concept was sound, but that stuff was a nitrate sink. If I HAD to do it again, I would put it in a mesh bag so I could pull it out, clean the bottom of the compartment, and clean the rubble. It gets nasty and nasty isn't good in this hobby.