I can answer number one real quick:
This shows where you can change portal manager to launch when a user logs in: https://help.landesk.com/Topic/Index/ENU/LDMS/9.5/Content/Windows/portal_t_configuring.htm
Then just update the agent for that group!
Thanks for the reply Joe,
Looking at the agent settings for portal manger, I see you can set it to start Maximized but there doesn't appear to be a setting to start Minimized. Any workaround for that?