Lola, when she did have an accident in the crate, would pee on her bedding, so we'd wash those in bleach+detergent. We would wipe down the crate tray with detergent (dishwashing usually) and then spray with antibacterial cleanser, all while it was still in the crate. that was easier than taking the tray out for us since the crate was in a built in nook under a desk in a spare room. Don't worry about accidents here and there, you have a very very young puppy. I think Lola was still having the occasional accident at 6 months.
How big is the crate? It should only be big enough for the dog to stand up, turn around and lay down.
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Bruno the Bulldog - Rest in peace old buddy.
July 1996 - December 2007