My 1 year old only whines in the kennel if she has to go potty. I never let her out if she is whinning. She loves her kennel and is totally potty trained. She lets me know she has to go with a little whine but just for a second or 2. I never let her out when she is whinning or if she continues to whine (which she doesn't) she knows being quiet is what gets her out not the whining.

As for teaching your dog not to be scared of thunder, will require a postive coming from the scary thunder. Everytime there is thunder treats literally fall from the sky. You should be sitting there reading a magazine and when you hear thunder you throw treats on the floor for her. If you really want to train this then go get a CD that has thunder on it and play it during your training session. Play the CD for 1-2 minutes giving many treats ( use something low fat like cheerios so you can give lots but won't make your dog fat). Stop the Cd play with her for a few minutes and start it up again. Good luck and remember with any training this will take time and patience.