When using the batch API, can I setup multiple batch jobs or can I only setup one batch with multiple operations?
You can call batch_set() more than one time, and batch_process() will execute all the batch sets that have been set with every call to batch_set().

Normally a module will call batch_set() once, and pass as $batch['operations'] an array containing all the functions to call, but if two different modules are setting their own batch sets, they will be both executed.