I've worked in an environment with mutiple domains twice. The most important point is trust relationship between the domains and DNS,
I had no problems because trust relationship between the domains was configured. Machines have to resolve the SMP hostname too, so you have to configure your DNSs servers properly.
To install the agents, if the domain relationship be configured, the Altiris service credential will works to install the agent in the new machines. Also you can configure a GPO to install the agents.
Regards,