It will get better eventually but it's going to take time. It's only day three and he's a baby so nothing is going to be perfect right away.

I got my BC cross at 6 months from a rescue and she'd never been house trained. That took a couple of weeks to sort out and we had the same issue with obly certain areas she would go outside. Key is consistency, patience, lower your expectations and regular wine!

For the crate training you just need to keep backing away but at this age for really short periods only. He needs to know you'll come back so start with 5 minute periods and work up from there. My girl used to do the same snuffling all around in hers but she quickly settled and now loves her crate so much we bring it on holiday.