I do not see my atlas in TPHelper drop down menu.

Your atlas wasn't registered by TPAssetProcessor. 

  • Did you put atlas file inside Resources folder?
  • Is data file has "_data.txt" postfix?
  • Did you use Unity3D format when generating atlas in Texture Packer?
  • If you steel have the same issue, please contact me by e-mail.

I have the big performance hit when instantiating character with TPSkinnedMeshTextureEx or MeshTextureExattached, how to fix this?

It happens because the script creates the new mesh with recalculated UV on Awake. That makes you available to use the same mesh for different textures. But this kind of behavior can cause the performance hit on object Instantiate. Problem is most actual for big meshes, characters for example.
You can fix this by checking "Use Shared Mesh" on TextureMesh component. It will remove mesh recreation and UV calculation, but you would not able to use this mesh for different atlas texture.

I've create second material for my atlas with another shader, but I can not assigned it to the model.

Uncheck "Replace Material" on TPHelper component. Now you able to assign any material to your model.

After importing your tools, is it possible to move them to another location?

You can move it anywhere you what to. It absolutely not place related.
The only one exception is Asset/Plugins folder. Unity will not look for Editor folder there. If you want to place this tool insideAsset/Plugins folder, then you have to move Editor folder of TexturePacker in any other place.

I try to replace a texture in TpMeshTextureEx on the Play mode, it just switches variables(tx/texture) but it does Not refreshes The visible texture/result.

After you change texture name or path to the atlas you should call applayUV function of TPMeshTexture component. It will recalculate UV and you will get the visible result.