Unfortunately without seeing how the character is made up it's impossible to say exactly what the problem is.
Generally you work with two types of characters in CTA4. One is standard characters which have a pre-defined bone structure, and the other is Free Bone characters where you create your own bone structure. Free Bone characters are great because you can literally animate anything, but the downside is you can't use standard motion clips with them. A Free Bone character has to be animated manually.
From your description it sounds like your character is not adhering to the standard character structure which may be causing the problems of breaking up.
If you intend to use the PSD workflow I would advise going through some of the character creation tutorials like the "Animate A Character From 6 Body Parts" on the page below. These should help you ensure that your character has the correct bone structure that will match with the motion clips you wish to use.
https://courses.reallusion.com/home/cartoon-animator/pipelines-and-render/photoshop
Peter
Forum Administrator
www.reallusion.com