I just got my hands on some Mopar Performance Headers that I wish to install after I get smogged, but I was told that there could be some issues with the powertrain control module. I have a 99 Dodge Ram 5.2L Auto. I have no idea what to expect for when I do this installation. Can somebody give me some insight as to what I might expect?
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If these are the shorty headers that are a direct replacement for your stock exhaust headers, just do the replacement. You won't have any issues. Your engine PCM will learn on it's own in a relatively short time how to deal with the increased exhaust flow.

If they are long tube headers you will need to do some exhaust modifications to allow the catalytic converter and O2 sensors to still be mounted. The PCM uses the O2 sensor readings to adjust for fuel and timing.

Do a search here in the 2nd gen forum for header replacements as there is a lot of info available.