My answer is... you can't really prepare your heart for the changes that are going to happen, but you will adjust. Keep in mind that the best thing you can do is to support him and write him lots of letters. Having gone through Basic Training myself, allow me to tell you that the drill sergeants try and let everyone know there's a good chance their relationship will not survive the separation. If you intend to see your marriage through, write a lot of letters and let him know you still care. Tell his friends and family to do the same. Mail call is a very lonely time when you don't hear from anyone.
As far as your son, kids are remarkably adaptable. Put a lot of thought into a way to word it that you believe your son will find most easy to understand, but don't say he "went to work" or your hubby will never be able to go to work again without your son feeling anxious. Tell him "Daddy had to leave for a while, but he'll be back," or maybe "Your Daddy has a very important job to do for our country, and it means he won't be home for a while." Something that lets your son know that it will be all right. After a few days, he'll get used to the new routine, and he'll be all right.
My son was only three months old when my husband left for a 1-year deployment, so I can sympathize. If you need to vent, feel free to e-mail anytime.