Here are the answers to your questions (Updated to CESM 1.5)
What command line arguments can I use when installing CIS that will stop it from restarting the client machine? Users will not be impressed if I reboot their machines during the install.
1. Now user is informed about reboot with system message. Reboot is delayed for 3 minutes. It is enough to close and save documents.
Is there anywhere to configure the update schedule and location or is this predefined?
2. CIS 3.11 now does not downloads any updates right after installation. You can configure them to download updates from Comodo Offline Updater (which is the service providing updates for computers in intranet) and update CIS.
Is it possible to use CESM to connect to workstations over the internet? eg one central CESM server which manages policies for seperate networks over the internet without VPN?
3. It is possible if you have static IP and properly connected DNS. I.E. if you can connect to some ports on target computer/server it is possible to work over Internet. But better - use VPN