Here in spain is almost the same to be married or not.
If you go through separation you should look for an atorney in order to prepare the separation document rules.
Most of cases your partner will got the rigth of keeping the hause to live in with your son, and you will have to paid a rent for him to get feed. The account will depend on the money you earn (250/ 300 euros per month is a regular account for your son)
If she does not work and he proves that in the last years she has used her time taking care of the son, she can also ask for a rent for her, wich will depend on your incomes.
In the rules you will have a visit plan to have the son with you on weekends, holydays and so on...
If it is not possible to get an a personal agreement the juzge will mark all the points.
So, look for an attorney, and he will explain you wich are the betters steps for you to do, once he has study your personal circunstances.
Best regards, XXXXX XXXXX question if I had been clear enougth.
I will try to answer you any question you laterly ask, anyway. Sorry for my bad english.