You may be switching the food too quickly and no...kibbles and bits is in no way a healthy food! Here's a link to another thread on YT that discusses dog food scores...the ones with the higher scores are the better foods.
http://www.yorkietalk.com/forums/showthread.php?t=64979
We used to feed Innova but switched to Nature's Variety raw and I also (currently) use Dick Van Patten's Natural Balance dry kibble which is an excellent food...it can be bought at Petco and it's not too pricey. We didn't have any smelly issues with Innova and we don't with the foods we use now either. I think the smell comes from ingredients like corn and lots of fillers...with a better food you won't have that and they will only go once or twice a day, it will be firm and easy to clean up. Good luck finding a good food for your baby.....