I can definitely relate to the beagle dilema, I have been there done that twice now. It was the separation anxiety that was the hardest, the whining, crying and howling. The crate thing, well let the pup get a little use to its surroundings. Crate training is a huge success, it is important for the baby to respect the crate as a private lil space for them. It is also important not to leave the puppy in the crate with barf or pee or poop for too long. As for the peeing outside, stay outside with her until she goes, probably approx 20 minutes after a meal and drink.
Dont shoot the dog is a great resource, it is a book.
Also someone mentioned the Kong, that is a great resouce, I have also found the "triple crown" everlasting treat ball is great. I have 2 beagles and that keeds them entertained for a hours.
Also looking for a resource guide on the net, where you can post and get replies from other dog people, Doggiedoor used to be a great info site.
Stacie