Complex mesh with armature and mesh deform modifier Warning: Many pictures! May be annoying... ;)

I'm trying to build together a rig where I can animate with armature most of the times, and fix something or add some specifics with mesh modifier. There are 2 problems with that. Let me explain my setup.

To represent my complex mesh I've created a cylinder.



Then I've assigned 2 vertex groups



Then added 2 cubes to represent my mesh modifier cages.



Then added mesh deform modifier to a cylinder to modify it with cubes.



Then added armature and rigged cubes.



Works good. My result is something like this:



Not quite what I want, but now I can go to edit mode and fix whatever I don't like. I can even animate changes with animall addon, but not with an ease that I would like to. So, I've added a hook.



Ok, but now whenever I use armature, hook stays in place.



Still can modify mesh with hook, but something that stays out of place would be bad in a real complex mesh situation. Just imagine 20 hooks are out of place and you don't really know what changes what... I tried to parent, to copy transforms, etc.,etc.,etc., but to no avail.

Right now, I am manipulating a cage that is manipulating an object. So the 2nd problem comes when I want to manipulate an object directly with armature, and then fix with mesh deform modifier.

If I rig my model and not my mesh cage, then whenever I move my object with an armature the cage obviously stays in place like a hook, creating a mess and if I rig both, then it's obviously doubles all the deformations



Is there any way to do it right?

Blend File if needed: Test.blend
Your use of mesh deform is not really warranted here in my opinion. Keep your bones, maybe subdivide them into many smaller bones (in edit mode, "w" -> subdivide). Then, change armature to object mode. Select cylinder, then shift+select armature, ctrl+p, "with automatic weights".

This should give you a nice smooth deformation.

If you are going to use mesh deform, why do you use 2 cubes. It should be one mesh. I think a better explanation of your exact problem may assist in answering in a more detailed fashion.

I will add another note. Maybe a better solution for you is to use shape keys to correct issues after armature deform. There is another method, add object -> lattice. In mesh panel subdivide it more. Then add modifier to your object -> lattice and select the lattice you created as the source. You can parent the lattice to bones just fine.