either one job deploys the wrong content (because the package got modified out from under it by the other job) or you get some kind of error w/ the package object locked because the other job is making the change.
can you create 2 packages? can you do some parameterization in the package so you don't need to make changes? what are you deploying that you need to modify at deploy time ?
Files and their paths may be different for each deployment. We may have to create different packages or figure it out the way to parameterize them.
What happen if two users execute/start the same jobs?
look into parameterizing and properties.
if 2 users start up a job at the same time, depending on what the job does, the 2nd may fail or the 2nd may wait for the 1st to finish.
if you run a job, change the targets of the job and run it again, you should have 2 copies of the job running against a different set of targets. (i think you need to enable parallel job mode for this to work though)