Crate training a shelter dog?

I am considering adopting a young dog (under 6 months) from the local animal shelter. I have found a wonderful girl who I think would fit well into our family. She will be an indoor dog, but as she is in the shelter, I'm not certain whether she has had any training or housebreaking.

When I took her out to walk and play with her, I saw that she should be quite easy to keep in a kennel - she didn't try to dash out of the kennel before I was able to get the lead around her neck, and when it was time to bring her back inside I walked her right up to the door of the kennel and she hopped right in when I told her that I needed to fill out the paperwork and that if they'd let me adopt her I would be back to pick her up on Thursday (Yes, I talk to animals).

However, at the shelter, they are kept in the kennels most of the day and only briefly walked by volunteers or when a potential adopter comes to see them. So, I am concerned that a shelter dog may get somewhat accustomed to doing their business in a kennel.

Does anyone have any advice on retraining a dog if whining, barking and other behaviors aren't the issue, but the dog finds it acceptable to go in their kennel? I will need to kennel her while at work (but will be going home in the day to check on her and walk her), at least until I am certain that she is accustomed to our home and won't get into wires for electronics, chew on furniture, etc. I don't want to discipline her for accidents in the kennel, as she seems otherwise to be very accepting of kennels and I don't want to create any ill feelings toward the kennel. But I'd like to minimize kennel accidents, not just to keep from cleaning them up, but also for her comfort and cleanliness in the kennel while we are away.

Additionally: The kennel she is in at the shelter is in their "puppy" room. It is one of the larger kennels in the area, but she is a medium sized dog and they are guessing around 6 months, so it's large enough but not so large that she has excess room (i.e., not really enough room for her to have one area for the bathroom, one area for eating, etc.). My kennel at home is quite a bit larger than the kennel she is in (rated for a dog up to a grayhound, but I don't really think a grayhound would fit comfortably), but I still don't feel it would have enough room to put a puppy pad and her still have plenty of space, although I will probably try lining the kennel with puppy pads if she does have accidents. I'd prefer gentle methods that ensure that she seperates the potty from the kennel entirely.