Have you decided, in your mind and heart, if you are separated or not?
That's a big challenge, and a hard one. You've taken some steps to be physically separated. You're living apart, although he does visit for the sake of your kids. If he's coming over to help with the kids, then that's what he needs to focus on when he's over.
When you're living apart, it's a lot easier to set up and keep boundaries. If your mind is in turmoil and you're not so sure you're there yet, it is going to be hard to do that. The biggest challenge will be disengaging. He starts getting into an argument ot starts trying to pick a fight, then shut it down. Let him know that you're not talking about that. He came over to spend time with the kids, and he can do that or leave.
That's one thing you can do - don't allow yourself to be guided into those arguments. It does sound like that's what you're doing and it takes a lot of work to get there. If you're still struggling in your mind and heart it's going to be a challenge for you, but it gets easier with time. Just decide your boundaries that you need, and don't let him cross them.
As far as your son, I wouldn't think you need to go into detail, again, about your concerns and why you're taking him to a counselor. You've already told him your concerns. Based on that, you've decided the route of the counselor. You can simply let him know of the appointment and that you're doing what is best for your son. He can come to the appointment, or he can choose not to. End of discussion.
Keep your boundaries strong, and do your best to stop concerning yourself with how he will react. You know he'll react at some point, and you can't control why or when or how. You can control how it affects you and you can distance yourself from that fallout. He's a grown man. He's gotten himself into the position he's in. He's going to have to just flail around unti he understands that - it's not your duty to guide him to that. So let him flail, and keep concentrating on you and your son.
Until you get your heart and mind on the same page, it's going to be difficult. That's what this place is for. That's what al anon is for. Transitions are always rough at first, but they'll get better by working on and working through them.
I found, in my situation, that sometimes direct communication (talking in person or on the phone) was almost worthless. I ended up setting up a different line of communication - text or email. I'm not sure what possibilities are there for you in your situation, but I know it helped me to not engage in the back-and-forth arguments. And of course my own situation was different - no kids, etc., but it was easier for me to communicate that way some times because I could get to the point of what I wanted to say, and there was no immediate feedback or opportunity for interruption or change of subject.