It was suggested that I try to put my boys litter box UNDER their hay rack but they didn't approve of that as it hindered their running laps against the coroplast. Because of that and the hay they were scattering and wasting, it wasn't pleasing me, so I thought of a solution (I can't currently make them a 2nd level kitchen area and I'm not quite sure if I want to anyway LOL);
I bought a sheet of coroplast from Lowes, had it scored and cut to make a box. The sides are low enough they can hop over it but high enough to contain "waste". I had an extra wide piece of coroplast that I taped to one side and then hooked their hay rack to it. The box is large enough for both boys at the same time but is slightly smaller than their cage so it still allows for laps around the cage directly against the coroplast. They seem to approve of their new kitchen as I haven't heard or seen them trying to rearrange.
(If you look really close, you might see 2 boys playing peek-a-boo at the front of the cage LOL)
(And just because I thought this pic was too cute NOT to share. This is their assumed treat area )