Analyze the script. Before launching into a make-out session with your scene partner, make sure that the script calls for it. Read the script carefully and discuss with your director what exactly would best serve the scene. It may be that a tender moment would be stronger than a graphic one. Or that an intense beat will actually do more than simple romance. Whatever the physicality is, make sure that you, your scene partner and director are on the same page and in agreement about what is to be expected. This will make approaching a physically intimate scene more comfortable.
Clean yourself up. One issue that can make a physically intimate scene uncomfortable is poor hygiene in the form of body odor or bad breath. Before you force your scene partner to get up close and personal with you, make sure that you are presentable. Bringing deodorant, toothbrush and toothpaste or mints or gum to rehearsal will make you a pleasant person to be intimate with.
Check in with your partner. It's easy to get caught up in an emotional moment while rehearsing or performing. You may find that you do things in the moment that you weren't planning on. Or, you may discover things about your character that you want to try out when it comes to your physicality. When you have a moment, ask your partner what he or she thought about your work. While you don't want to get into a situation where a fellow actor is giving director's notes, you do want to give your scene partner the chance to let you know if they are uncomfortable with anything going on on stage.
Enforce your boundaries. Just because your scene partner gets to be hands-on with you on stage doesn't mean that should be permitted to carry over when the rehearsal or performance is done. Make sure that your partner knows what you are and are not comfortable with--on and off stage.