Fusing meshes into 1

Hi, i’m trying to fuse 2 meshes that are in the same spot:

They are on the same spot but aren’t the same, so when I use the Automatic Weight Paint, this happens:

Is there any way to solve it?

try selecting all the loose edges in edit mode, and clicking ‘remove doubles’ ( in your tool shelf on the left )
(edit) also, your model looks good, but your topology looks very messy. there could be deformation issues when you try to animate it. also potential for shading artifacts from non planar quads, and long triangles.