Short answer, there is no procedure for Chrysler Vehicles, that includes the Commander. The PCM will learn its adaptive settings on its own, in most cases, when the PCM dumps all its volatile memory, the engine may stall after the first start. If the engine has experienced wear or behind on preventative like spark plugs and air filters, the required tune may vary greatly from the baseline reference engine. If that is the case, it will take some time for the PCM to make adjustments and find the right correction values.
The best way to help the PCM to learn all the corrective values, is to just drive the vehicle in a variety of conditions, stop and go traffic, steady high way cruise at various speeds for a few minutes each, mild acceleration, moderate acceleration and full throttle accelerations. And it will a need a few warm ups after fully cooled down as well.
If you're still having problems after 75 miles of a variety of driving, plus a couple of warm ups, then you need to start troubleshooting, diagnosing, cause the PCM should have learned enough by then that you don't have idle roughness or stalling.
Have you inspected the air filter, and when was the last time your plugs were changed? If you're idle is rough and you stall, no codes, and you're overdue for a plug change or have a dirty air filter, that is likely your cause.
EGR's can cause idle and maybe even stalling problems, and they sometimes don't throw a code when they fail, that is something else to keep in mind.