I have my three dogs crate trained, and I didn't have any real issues with it. Learn here
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I didn't get them as very young puppies, and that makes a difference. young puppies are like young babies. They don't cry to manipulate, they cry to have their needs fulfilled. They need to potty every 2 to 3 hours at this young age, and crating them for long periods of time causes them physical discomfort. They don't like to potty where they sleep, so it creates the need for the dog to get out of the crate, or soil it, which will make him more reluctant to use it.
Make the crate a place where good things happen. My dogs get a small treat every time I crate them before I leave. They also get fed in their crates (I feed a raw diet, so it's less messy if they eat in their crates). They dive into their crates in anticipation of food. I also leave the crate doors open all the time so they can sleep in their even when I'm home if they choose. If you have a smaller sized crate, keep it close to your computer, or other busy areas of the house so the dog has an option to go there and rest when you are home. toys such as Kong's are great for the crate because you can stuff them and give the dog something to occupy him. I used to stuff mine with a mixture of peanut butter and frozen mixed veggies, then I'd freeze it before giving it to the dog. You could very easily do this when you are sitting at the computer, give him the Kong in the crate. Shut the door and let him enjoy it while you surf the web. (he may have to potty after he finishes it, so make sure you take him outside when he's done). I'd also remove the kong and take him out of the crate before he asks to come out.
If you keep it positive, don't make a fuss when you come home, or when you leave, and have patience, the crate can be a wonderful tool!