I had the same issue with my 7 year old. For the first 4 years, I allowed her to sleep in my bed. Almost every morning, there would be a present for me in the living room. So I began to crate her at night. Soon, she was soooooo happy to hand her item little palace to govern (as all queens do, haha) that she began to ask me to allow her in the crate during the day so she could hang out in there! So I decided that I would just leave the crate door open all day so that she could come and go as she pleases. At night, I tell her that "its time to go to the house" and she prances in there. I close the door and cover the top with a blanket. I believe this is sort of an innate feeling of security that dogs enjoy.
Hope this helps. And dont feel like you are doing something wrong. Behavioral heath is a key component to overall well-being and will prevent any tension between the dog and the master (which is what the dog's main concern with life is anyway).
As for the did, I suggest getting a prescription to a Science Diet regimen, or choking for him as posted above. Most dog food from the store with be loaded with corn, which not only has almost no nutritional value for a dog, but also expands in the gut, causing an increase in frequency of defecation.