Multitexturing models

[ManuelVonK03]

Hey everyone,
I am new to LWJGL and I've just learned how to texture 3D models using the same texture for every face. I downloaded a 3D model as a .obj file with several texture files attached.
I read about putting them all together in a texture atlas, however this would change the texture coordinates. Changing them manually is not an option since it is a rather big model.
Perhaps it is possible to import the .obj file into Blender along with the textures, having Blender create the texture atlas and adapt the texture coordinates.
How do I deal with these multiple texture files?  Can someone help?