I would definitely recommend the Diaper Free Baby book and website (www.diaperfreebaby.com).
My son is now 17 months old and partially potty trained... we are taking our time and enjoying the process. My son would pee successfully, but would not have a bowel movement and would be reluctant to sit on the potty when having one. As I watched him, I sensed that look of embarrassment on his face when he was having a bm. So, I altered my approach. Whenever I saw him having one, I wouldn't rush him to the potty, but would go up to and speak quietly to him and tell him that he is having a bm and that it is ok and that he should not be embarrassed... I did this all the time before trying to get him to the potty/toliet. It was also great if he wasn't wearing pants/diaper and then he could see it come out and we could look at it. Then, I would clean and we would take it to the toliet together. I also made a point of taking him to the bathroom with me whenever I go... when I am having bm, I would let him know and let him look in the toliet before I flushed it. Now, sometimes he has his bms in the toliet/potty... and other times in the diaper, but he does not seem embarrassed like he did before....
In your case, I would really try to tune into what the issue is... and go from there. He could be embarrassed, or maybe his bowels just move quickly without warning... my son is much more successful at holding his urine than his bms... It is so great your son is peeing in the toliet... just be patient... it sounds like you are doing a great job and your son is defintely on the right track.
Ah! One other thought: maybe he needs to be in more of a squatting position like toliets in Eastern countries vs. toliets of Western countries (where we sit). Maybe try letting him have his bm on a piece of paper near the potty/toliet... maybe it is a positional issue. Then you and he can try to adjust to having a bm while sitting vs. squatting? Just a thought.