Hi KL,
I'm sorry that you are going through this - my heart goes out to you.
I like the advice from Lesley B - keep it simple and tell your son what is going to happen and nothing more.
And remember that you will have to repeat it 8 million times. That's ok - just ALWAYS give him the same answer and he will learn that you are consistent.
One note - please try to find a way that you can work this separation to YOUR advantage. That will make you less resentful (and I know it's hard to do, but it may make or break the separation for YOU). What is it that YOU have wanted to do that you haven't been able to do while you were married / in the last year / since having your son? Join a group, paint the house, travel to wineries, get some girlfriends, start a cookie baking business. Whatever it is that will start to make YOU fulfilled REGARDLESS of what your husband does. If he sees that you are happy WITHOUT HIM, it will do more to fix your marriage because he will want to be a part of the you that is happy?????
I'm not sure if you are still seeing a counselor - but I would set some parameters for the separation.... what does HE want to accomplish during the separation? What do YOU want to accomplish during the separation (for ONLY you.... let him worry about him). How often will he see his son? How often will you see each other? what about money? Will you see other people? When and how will you talk about where you go from there. Don't just have him move out with no plan.
hugs to you and your son and your husband that you find peace.