It does not matter how standby was setup.

When you are ready to upgrade, make a note of your latest log file and make sure it applied to the standby database. Proceed with the normal upgrade steps, after you done with the primary upgrade standby server (only software portion of course) When everything completed your standby database should be able to accept archived logs from primary.
Also look into dataguard configuration, you do not need to use shell scripts to move archived redo logs , arch or lgwr will take care of this.