When we go with fear based on assumptions instead of facts it can be a monstrous mountain to climb and become so threatening to us we just stay stuck.
Please seek out legal counsel on what your options might be but please DO NOT stay in an un-healthy situation for yourself and your children out of fear of him having them alone.
Sometimes more emotional harm is done because you stay. No matter what your reasons may be, no matter what your intentions may be in keeping them safe from him and his alcoholic/drug behavior, staying with him while he is actively drinking/drugging will certainly have an affect on your children’s future relationships and an affect on YOUR future relationship with them. Often the children of alcoholics resent the parent who didn’t drink more because they did stay and kept the children in an un-healthy environment. Al-anon rooms are filled with second, third generations of people who grew up in an alcoholic home, married an alcoholic and struggle with relationships.
At the very least see if you can get yourself and your kids some help, it will also help transition them/you through a separation and a potential divorce.