Humm if set up right then there should be no conflicts as to an “expected” result and I’m assuming that your attempting facial animation?
With out seeing the source material it’s just all guessing in the dark but Skin Morpher Edit Poly out of 3ds Max is all that is required and how I have things set up so as to not run into cross platform comparability problems which is usually the root of the problem.
Since you don’t state what conflicts you are having, or a video of the result, then an understanding of the requirements might help.
Morph targets is nothing more than an offset of the world location of a vertex relative to the local position as an XYZ value that is recorded as a difference. In notion form the value would be Vertex ID,X Y Z so in long form a single value would look like.
Vertex ID: 123
X value -10
Y value +5
z value +30
This means that “only” the vertex data that has changed from a XYZ value of 0 needs to be recorded with out the need to store the entire vertex set of a given object.
Morphs are also additive rather than absolute so if you add value changes to the morph all areas effected that are not 0 0 0 will become additive as to the final result and would appear to the viewer as an unexpected result or conflict. In context if X is +5 on one target and X is +10 on another the finale output would be +15 and will compound with each target added.
By it’s self the unexpected result of a target can be backtracked as to what area a given target has influence over.
Now if you add a joint, bone, into the mix then it should have zero effect unless the joint “changes” the local XYZ reference location of the vertex data influenced by the morph, which we now know is additive,
Combining both Skin and Morpher is the “clean solution” as to the need for facial animation as both work independent from one another as to some simple rule requirements to ensure a predictable result.