For the jobs that are on the same SQL Server, I just use the sp_start_job command, but I can't do that when the job is on a different box because it's not apart of the sysjobs table. Do I use the isql.exe or an equivalent?
You could use the command line tool. Before going that direction, you may want to consider adding a linked server to the remote server. You would then be able to call LINKEDSERVERNAME.msdb.dbo.sp_start_job.
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