My logical decisions come from my existing knowledge. I may not know everything about the topic at hand, but if I know, maybe half of the puzzle, I use my intuition to fill in the rest. The solution has to make sense.
For example, right now, my community is talking about closing one of our elementary schools to save money. The community council has stressed that everyone remain logical and unemotional in their arguments about which school to close. The school board made up three criteria for closing a school. They use ONLY those criteria for closing a school and call themselves logical and unemotional. As a very rational person, it was obvious to me that the members of the school board were anything but logical. As an INTJ, I think the more information you have, the better logical decision you can make. One of the school board's criteria for closing a school is the age of the school. They want to close the oldest school in the district--without considering other factors concerning building quality. The school in the cross hairs is well-built, but old. One other school has crumbling foundations. Another school has a leaky roof with fungus. But the criteria for closing a school only takes age into consideration. How is that logical?
I think it's logical to make informed decisions. You should try to be objective and unemotional about it, and you should have as much information as possible. As an INTJ, I sometimes skip past gathering all of the information I can because of my strong Ni. It's too easy for me to fill in the gaps. But I still believe that being informed is essential. Looking at all sides of the issue is also important to me. I love brainstorming solutions, and I can come up with several alternatives quickly. If you have difficulty making logical decisions, try making a list of pros and cons. I almost never do that. I just KNOW the logical solution like some people KNOW that their spouse is their soul mate or that god is real. But it's a good place to start that isn't overwhelming if you have trouble making logical decisions.
As for emotion, I think it can be very important to decision-making, especially when the decision is emotion-based. Emotions can be just another consideration in your decision. I had to decide where to go for grad school. I looked at cost, level of prestige, field of study, and location. All of those considerations were important, but an emotional consideration kept me from moving too far from my family. That doesn't mean that my decision wasn't logical. It was logical for me--and for my personality type. So yes, I think emotion can be an important consideration. I just don't think it should be the only consideration. If, say, you were in an abusive relationship, the emotional decision might be to stay with your partner because you love them. The logical decision would be to get out of the situation no matter how hurt you may feel--emotionally--because of it.
Anyway, to sum up, I think logical thought process for me means being as informed as possible and knowing what you're getting into even if it is a decision influenced by emotion.