If the Power commander has a USB connection (one of the type III has), you can plug it into a computer and upload a map to it. The software and maps are on the power commander website.
Software for your pc here:
http://www.powercommander.com/suppsoft.shtml
Maps here:
http://www.powercommander.com/suppsuzmaps.shtml
I'd strongly recommend you get it setup properly on a dyno if you're going to change the filter. Each bike is different and even if you find an exact match for your exhaust/bike/filter the downloaded map might not be perfect.