Beginning training

Before I go to far I need to amend somethings, as I stated we are using the crate method to train house break Remy, I said things were going great, I just wanted to let you know I may have overstated things, so I will correct myself and say things are going well. I just do not want to give anyone the impression that my dog is super duper yet. Remy has an occasional mistake but so far it has only be a little pee pee. When she makes mistakes we do not strike her but admonish her with a stern "bad dog!!!" which seems to shame her and let's her know we are displeased.
As a family (my three boys and my wife) we have been working on basic commands such as sit, come, stay and wait. She is doing alright so far sometimes she is a little hard headed, when she is not listening we try to get her attention by stomping or making a loud noise and then repeating the command in a firm but calm voice, when she listens we give hearty praise and offer treats on alternate consecutive positive responses. We generally work with her for 15 minutes at a time twice a day., and we try to make it fun for Remy and the family, and so far it seems to be working out for everyone, I have noticed that after training the kids are more involved with her during freestyle play time which generally follows our training sessions. We are having a harder time with the stay and wait commands but I am noticing improvement in those areas as well. At feeding time I will generally set her food out in the garage before I let her out of the house and have one of the kids let her out before she gets at the food I will block her call her name and say sit, and then wait I will continue to block her until she complies and the give her some more of that hearty praise she seems to love so much and the set her loose on that tripe. Lately I have also been trying to meet her at the door and give her the stay command backing up two steps at a time until we reach the food and then giving the wait command. I am trying to work in small steps but continuing to build upon what we have been learning.