It's so difficult being a step-parent... I know the feeling well. We sometimes see thing we think should be done differently - definitely things that affect OUR lives! - and we sometimes try to help ... but the fact of the matter is that we often cannot parent our step children.
I would advise you to have a serious discussion with your partner when her child isn't there; maybe take her out for dinner or whatever, discussions about sensitive topics are sometimes best done away from the home environment.
Tell her how you feel, how the situation affects you but even more importantly how you are concerned that it's not good for the boy. Tell her you will support all her parenting decisions, and put your thoughts to her gently and thoughtfully, and hopefully she will see things a bit clearer.
In terms of making the changes - deciding to have the boy sleep in his own bed etc - it will have to be his Mom that takes action.
