Cage Newbie needs help thinking through cage design, long!

We are new owners of Chrysanthemum and BJ, adopted from a local rescue last Saturday. I've been on this site since April researching about guinea pigs.

I used wood shaving that the rescue gave me for about four days before I was able to switch to fleece on Wednesday.

I have a 2x4 with a 1x2 kitchen.

I put a sheet on top of the kitchen area so they feel a little more protected in that area, as opposed to being open. In the kitchen, I have shavings, though I was thinking of using Carefresh. I have a pigaloo and a grass hut in the corners opposite the kitchen.

Here is my dilemma - they really like to poop in their hiding spots. I think it's because they spent the first four days in our house hiding in them. For the past few days, most of the poop has been in the two hide outs, and only a little in the kitchen area.

Question #1: Can I just use fleece in the kitchen area? Do I *need* disposable bedding in the kitchen area? Do I even need a separate kitchen area since they aren't pooping in that area? Should I just remove the kitchen area in just keep the food to that side? (One day, if I feel up to it, I might add a 2nd floor kitchen - so I'd keep the coroplast kitchen aside when/if that day comes.)

Quesiton #2: Should I use disposable bedding under the pigaloo instead. I was thinking of putting pigaloo and bedding in a low cardboard box (like what you get at Costco). They move the pigaloo around, so I was thinking the cardboard box would help keep it in place.

Thoughts? Thanks for any advice you can give!