The Real-Time Process Explorer was introduced in SAM 5.0, which was about 4 releases ago. The current shipping version of SAM is 6.1.1, and SAM 6.2 is currently in beta. It would seem you're a few releases behind at this point and I would recommend upgrading as there have been a wealth of improvements since the product was named Application Performance Monitor (APM).
As for monitoring processes that aren't even running, I'm afraid you will either need to wait until the process is running to select it for monitoring, or manually configure a Process Monitor to watch for the specific process when it does in fact execute. Both options will work equally well. If the process is not normally running all the time you may not wish to see it marked as "Down" in the web interface. Currently this is not possible, but is a feature request you can vote on here.
Monitoring multiple instances of a process is inherently done in SAM, and a count of the number of instances of a process is shown in the WebUI and alertable through the advanced alert manager. If you wish to monitor specific instances as their own individual component monitors for alerting, reporting, or performance monitoring trending purposes you will need to specify the unique command line options each process executes with as part of the component monitor settings.