Jadey, such a sad story - must be truely horrid for you to watch those you love suffering.
I dont think you can have much influence with how the couple sort themselves out - thats up to them but you can support your Son in being the best father he can be and be a warm loving Grandma where your little GS can perhaps let of steam a bit as he gets older. Children need to have a listening ear when such events happen, and he will appreciate a place were he can have a good cry or moan without feeling he is upsetting his parents.
I suspect your little grandson is now old enough to begin to understand a little more about his life and thats why he is now getting upset. It will take a little time, but your son will need to see his boy as often as he can to spend time with him and let him know he loves him. As he gets older I am sure your little GS will begin to understand that although his Mummy and Daddy dont live together they do think the world of him. For what its worth I, personally, would be against them getting together if they really are not a happy couple, but thats just me.
As with complex family arrangement - we've all had them - it can all seem pretty bleak but they are usually just stages that have to be endured - and they will pass. I wish you all the best.