Hi Rehan,
For Shutdown;
Subs 1st followed by Pub
From cli
utils system shutdown
This command allows you to restart the system on the same partition, restart the system on the inactive partition, or shut down the system.
Command Syntax
utils system {restart | shutdown | switch-version}
Usage Guidelines
The utils system shutdown command provides a 5-minute timeout. If the system does not shut down within 5 minutes, the command gives you the option of doing a forced shutdown.
Requirements
Command privilege level: 1
Allowed during upgrade: No
http://www.cisco.com/en/US/docs/voice_ip_comm/cucm/cucos/6_0_1/cucos/iptpappa.html#wp1051058
For startup Pub first followed by Subs
Cheers!
Rob