You have a multitude of interfaces available to you for monitoring. Within LoadRunner itself you have the classical monitors, whhich include direct to database monitors, a few OS items and SNMP.
Within SiteScope (LR 8.0++) you have a wider array of application and OS specific monitors, plus SNMP.
With the AS400 you have RTE where you can enter a command shell command for performance metrics.
And finally the LoadRunner analysis tool has the ability to import data from externally collected monitors.
As you are on an AS400, if your AS400 has an IP stack and you have a supported native database, such as DB2, then you may be able to use a LoadRunner native monitor. Additionally, if your AS400 is a managed device using SNMP, you will also have SNMP available to you for the collection of system metrics.
The preferred monitoring interface is SiteScope, as the richness of the data available exceeds that of the LoadRunner data monitors. You still have the same options available to you as you would have with LoadRunner native, plus additional capabilities. However, in the case of the AS400 those capabilities are still likely to be limited to a supported service (such as DB2) or SNMP for the OS level stats.
With RTE, have you considered taking a single virtual user to issue commands to pull OS monitor data instead of exercising the app? With this model you can scrape the data off of the screen, as if you would be correlating the information s part of a business process, and then create a loadrunner datapoint to include the name of the monitored element and the value. This is usually a lot simpler to implement than SNMP monitoring and works quite well in TN[5250|3270] environments.
And finally you have the ability to import external monitor data. I tend not to really like this model very much as Loadrunner applies some quite odd names to the imported data sets. But this is capability is available in every version of Analysis available in the past decade. With this model you could run a script on your AS400 to collect monitor metric data during your test. At the end of the test you would then import the data into the Analysis tool to be applied alongside your existing timing record and monitor data. Be sure and look at the formats for the data import, for if you can get your AS400 tools to spit out data in the precise import form you need then you will be ahead of the game. Take a look under tools->external monitors in your version of Analysis for additional information.