I've got a scheduled job that runs a package every couple of minutes, and I also have a method in an application that calls a stored proc that can also execute the same scheduled job. My question is what will happen if I call the stored proc to execute the job at the same time that the job is executing on its regular schedule. Is it possible that the an instance of the package will execute in parallel?

SQL Agent jobs won't run multiple instancessimultaneously, as long as you are calling the same job.

Similar to above situation, i want to find out that if multiple job (long running jobs, schedule may overlaps between them) are being executed. Can i get timeouts in other queries/procs.