Alignment Issues

Over the past week I've gotten 100 frames of animation done, imported, and filmed in RCT3, and about 100 more animated only. The second 100 frames are proving difficult to import, because there are two different rigs interacting with each other. In theory, this shouldn't be a problem, because I have technically done the same thing in an older shot. When I did it before, though, there was one complex armature and one armature with only one bone. Right now I am trying to import two complex armatures. They don't want to import in the same scenery file, so I have tried separating them, but there are major alignment issues that I have yet to fix. As I write this post, I think I recall that when I animated interaction between two models before, I imported them separately as well. So I should probably focus my efforts on correcting the alignment problems, instead of trying to get both animations to import in the same scenery file.