I used shelving paper, like what you put in the drawers in the kitchen. Might sound kinda weird but it worked well and was very easy to clean. I had a water bowl mid-level and another large water tub at the bottom, iggy normally would do his business in the water at the bottom and I would just change it right after, once or twice a day. Here's a bad pic of the set-up, the shelving paper was a green and white marble pattern. There were 3 levels but you can only see 2 here.
I wish I had a better pic, to clarify, the cord was cut off the hot rock and I did lower the UVB bulb so it wasn't up so high.
If you do use indoor-outdoor carpet, get 2 pieces of the same size so when you pull the one out to clean, you can put the other one in. They need to be cleaned every time they get dirty (which can be daily).
If you have cracks that you are worried about mold growth, yes, you can use clear aquarium sealant. Just make sure to give it at least 24 hours or more to cure (follow the directions). With good airflow you shouldn't have to worry too much about mold/mildew. I also useda reptile safe cleaner (I use Quat Plus) which is also anti-fungal and helps retard the grown of mildews.
Good luck with you iggy!