We run all of our jobs in several environments and still use the SQL Server Agent or EM to run the jobs.  The key is the synchronization of the DTS package ID's across the environments.  We have DTS package that performs the elevation of changes by archiving previous version and then moving the records that store the packages from the MSDB database to the target machine.  This way the package id remains the same for all environments and does not affect scheduled jobs or execution of packages from within EM.  Instead of managing VBScript, we manage the UDL's and ini files local to the machines.