You can absolutely use your own textures but it's done primarily though the E3D interface.
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Although, in a more complex procedure, Andrew has a tutorial in which you can use your image maps within AE. Like if you wanted to add text to the side of an airplaine or something, it's best done that way. Or an explosive hole is done that way.Â
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He covers that in one of the more recent tutorials that came with his Jet Pack.
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Eric