jPCT doesn't handle textures for MD2 files. You have to assign the texture yourself to the loaded object. Usually, MD2s already come with a texture (sometimes in PCX format, which needs to be converted first). After loading the model into an Object3D, you just load the texture and assign it to the loaded object. That's all. If you are making the models yourself, then there are no restrictions on how the texture should be build/look.
To animate models imported from 3DS, you have the same options that apply to all the other formats: You can manipulate the mesh itself, use rotations and translations and build a keyframed mesh animation from the model. In the projects section, there is a thread about technopolis, which discusses some of this aspects at the end of the thread. Maybe that helps to make things clearer.