If you are really concerned, be open with him about it. Good communication is important for any relationship to work. As for dealing with the ex, there are a lot of things you can do. It really just depends on how you want to effect her. Personally, I would sage or saltwater my home any time there is contact with this person. Anything else you can find or do to get rid of unwanted energy she directs at you (people do so all the time just thinking).
You could work on shielding your partner. The best one I know of utilizes visualization of a pure white light. Sit and picture your partner standing in front of you. Visualize a beam of pure white light coming down from the universe and completely enveloping them. See it pulse and start to swell out, so that it expands well past their aura.
You could do a banishment. It won't make her visibly disappear (unfortunately) but should help direct her away from your's and his lives.
If for any reason, she comes into your home, blow some powdered vervain on her back as she leaves. It drives away pests pretty well ;)
If persistent, look into hot foot powder. It has many uses, but is especially good at driving people away.
I still suggest speaking with him about it. If he allows her to be part of his life this could be an ongoing problem for you, and will make it a bit harder to get rid of her. Best of luck!