I've been working on my 3d character in blender and have finished making a mesh and the character itself.
When I apply the armature to my character with automatic weights it gets messed up.
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This is because of vertex groups and weight painting. I just got through this myself. if you assign and select a single vertex group in edit mode and then switch to weight painting mode you can change how the bones affect the model.
You can find vertex groups in the data tab of the properties panel. in the vertex group section you can select a number of vertices and create a group. you can then name each group you create. for example
You could select all the vertices in the head of the mesh and create a group and name that group head. from here you can now weight paint your head vertex group.
To get to weight painting, make sure you have the vertex group selected in edit mode. click the menu where you choose edit/object mode and choose weight paint. this will allow you to paint on the influence the bone will have on the mesh.
Switch your armature to Pose mode and your object to Weight Paint mode, then select a bone, see what influence it has on the mesh, and bring some corrections with the brush in Add or Substract mode.
You can also bring some corrections in the Vertex Groups panel of the Data menu: when you've parented your object to its armature, it automatically created vertex groups on the mesh, each vertex group has the name of the bone by which it is influenced. Select some parts of your mesh and choose them to be part or to be deleted from some vertex groups (with teh Assign or Remove buttons) so that they are influenced or not by the bones of the same name.
You can make some parts only partially influenced by a bone / partially part of a vertex group, it depends on the strength of your brush or the factor you choose below the Assign / Remove buttons.