Isn't it just that you have to place items on tables or bricks or something? Was that what you worked out? I don't see anything wrong with answering your own question if you worked it out yourself later lol.
Also I have holes in my base that I never got around to dealing with but I'm pretty sure you can buy planks that you can cover the hole with, I think from the department store. But I've not actually tried it yet so sorry if this isn't correct, I think I read it somewhere... >.<
EDIT: Ok so according to someone else who seems to know what they're talking about, you need to defeat the elite four, and then there is a sale at the department store that you will see advertised on TV. Then you go up to the roof and buy "Solid Boards" or something like that, to cover the holes. Hope that helped :)
EDIT 2: Argh I just saw Pokeslash's link. It was hidden from view and I didn't notice, sorry I guess that wasn't helpful then lol