You have 25 chicks in something only 2 and a half feet by two and a half feet? Yikes. That's far too small for that number of chicks! My four are crowded in something about that size at four weeks..... so I give them lots of outside time when it's warm.
First, in any brooder, make sure their bedding material is thick enough, at least an inch deep, if not more. Use nipple waterers, and there will be no damp bedding from spilled water, plus it will not get mucky from chick poop and bits of bedding kicked into it. Good, clean water for drinking is much better fo them, too.
If the bedding doesn't get damp, and you add more to it as time goes by, it's like the deep litter method in a brooder. Well, not "like" but IS. Or you can change the bedding material every couple days or daily, if you so wish. But without the damp bedding, a lot of that smell just won't occur.