Yes you can. Actually it depends on what you want to stop then start. The only thing is that the program that you want to stop and start has to be able to start and start by command line. What I mean is that you can't stop a program in the taskbar unless you can send a command line and it stops all instances of the program. If this program is a database that needs to come down to be backed up, then there should be a way to do it with a command line. Check with your software manufacturer and see if they can help you with that.
As far as setting up BackupExec, if you right click on the job and edit the job properties, it will have two boxes in there that will let you put in a program to run before and one after the backup job. I suggest making two batch files and pointing to them here.
Hope this helps..
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