My partner has his Sun and Mercury in my 12th house, I read on a synastry program, that his Sun in my 12th makes me aware of the importance of subtle emotional and spiritual factors as a basic power behind existence. It also says that circumstances in the relationship suggest that an element of sacrifice or isolation is necessary for your true self-realisation. For his Mercury in my 12th - this can lead to an attunement of thoughts and ideas which can be useful to you both creatively and spiritually. You may find that communication between you is less than straight forward. I think to get the full picture of our relating I have to look to see if any of my planets aspect his planets which have fallen in my 12th house. My Mars opposes his Sun/Mercury in the 12th and my Uranus squares his Mercury/12th.
One incidence when I got very angry with him was when he went out for a meal with his family because it was the anniversary of his dads death. My partner told me he would be back at 6pm. Well 6pm came and no sign of him or a phone call, to let me know he would be late. I phoned his mobile but there was no answer, it was 10pm by this time and I thought something terrible had happened to him and I was in a very emotional anxious state, I phoned my mother for advice on what to do, I was nearly ready to phone the police. I left messages on his mobile for him to contact me. Finally by 11.30pm he phoned drunk and was going on about a family argument he was having, and never even mentioned why he was late or apologised for not phoning. My partner was making up lie after lie on why he did not call. Like he didn't know he had credit in his phone, he didn't realize the time. I was fuming with him because he spoilt my evening, I was up worrying about him when I could have relaxed for the evening, he can stay out late if he wants all I ask for is the decency to call and say you are going to be late. He said he had hardly had any drink, yet he was slurring his words. It's hard to describe he can tell lies so easily even though I can see right through him. My partner does not tell big lies but he has ease in telling lots and lots of little white lies to get him out of an awkward situation. This is how I have experienced his Sun/mercury in my 12th house with my Mars in 6th opposing them. Natally he has Sun Square Neptune, so his personalty at times can be evasive and hard to understand.
I have always wondered what the impact is of having other peoples planets fall in your water houses. My Mars falls in my partners 8th house, and according to the synastry reading I have a tendency to stir up some of the most profound and dangerous emotions in my partner. My Mars opposes his Sun. Apparently because he is the Sun - he handles arguments with dignity, while I with my Mars hit below the belt. The Synastry program told me that I will have to work on problems with my temperament in this relationship. Cheeky computer

But my Mars is square my partners Neptune - so why do I get so annoyed and angry - because he is being so evasive and hard to understand and trying to escape through lies to explain his actions. My Sun is in his 8th as well so as the relationship progresses there may be intense moments and crisis in identity.
I am not sure if it is more difficult to have harsh synastry aspects coming out of the water houses, or if the water houses represent sitituations more hidden - not sure about the 4th though because it is an angular water house and problems may be more obvious in this house. I still need to learn my synastry astrology so I am not completely sure I know the 4th house is the inner life, the 8th house is about power, sex, transformative experiences and the 12th house can be loneliness and great suffering and sacrifice. I always find the water houses the most interesting in natal astrology or in synastry.