IMO, your dog is in a world of double standards. You expect him not to mess in your bed, but he's just 3 1/2 months old and not yet housetrained. That's like expecting a toddler to perform Trigonometry. You can't possibly skip ahead without creating a solid foundation. The previous posters have all got it right on the spot. Your pup isn't yet housetrained; ergo, he can't sleep on the bed without messing. The key is not to purchase a crate and keep it there as a living room accessory but to actually utilize it every day.

From now on, your pup is not allowed to sleep on the bed. He sleeps in the crate. He eats in the crate. He will learn to love his crate. At night, he will sleep in the crate, and he will learn to stop messing through his own mistakes. Dogs don't like sleeping in wet spots just as much as we don't. Remember he's just a.. what.. 14 week old puppy? I think it's time to take a small step back. In the end, it will be a huge step forward