Crate setup - 2 month puppy w/coccidia

Hello,

Just got a new 3lb 2 month old jack russell puppy from the pet store. I've been treating her for coccidia for 4 days now. My cage I've had for many years is 36" L X 20" w. She goes #1 & #2 in the cage. She also does her business outside when I take her out. With no partition in the cage she goes to the rear to do her business. When I partition the cage to 20" X 20" she goes right in the middle and doesn't seem to worry about standing in it after all within minutes I clean it up. I put a bedding under pad in the cage that takes up most of the cage. I try to take her out every 1 to 1.5 hrs.

How should I set up my crate/cage for her since she has a diarrhea problem? Should I leave the cage unpartitioned so she can go to the rear and do her business and keep her laying area clean (until I clean it up) or have it partitioned? I've seen alot of doc that says not to crate train a puppy with the runs.

I spend the entire day taking her out, cleaning the cage with neutralizer and washing the pads. Should I stop using the pads and leave her lay on the metal tray?

I'm worried since she doesn't mind messing where she lays in the smaller partition, she may be hard to break once the coccidia has cleared up if I'm doing something wrong.

Thanks!!