If I understand you correctly you want to know if you can manually arrange photos that did not match each other. The answer is no, it is completely automatic, so the solution is to learn how to take (possibly more) photos so that Photosynth can't help but see how things overlap.
Think of it like this: each time you make a new synth, Photosynth is "seeing" things for the first time. It has never seen a picture frame or a wall or a table or furniture before in its life. It needs to look at things from as many sides as possible if it is going to "understand" their shape. It can't be just shots of things from the top, bottom, front, back, left, and right, either. It needs photos in between those positions so it can see how one side connects to another.
Think of it as if you had been blind your whole life and just had surgery so that you could see for the first time, then think of each photo as blinking your eyes open. How often would you open your eyes to understand?