i always tried to "let" my children experience their emotions. never told them "don't cry" "don't be sad" "oh, you don't really feel like that". even though the intentions are good, those messages are very destructive.
keep your message short, and you may break it up into a few different, brief, conversations.
also, children are most concerned with how the change affects them.
"daddy won't be living in this house, but he will be living a half-hour from here and will come to visit sometimes" or what your choice of words is. i would also caution against telling your son something that very well may end up not being true, e.g. "daddy will pick you up every other saturday." it sounds like he is not very dependable.