It's nothing to be scared of--the coding, I mean.
Absolutely, there's a Federal Register from around the HIPAA implementation dates that might be of help to you. There was a discussion between the Federal level HIPAA experts and the mental health community over whether "coding was in DSM or ICD-9". This Federal Register established that ICD-9 is the official reporting system--per HIPAA Uniform Data Set. Guidance in ICD supersedes any "coding" done in DSM-IV.
Federal Register, November 15, 2004.
Essentially, providers diagnose patients in DSM-IV. Coders are supposed to code in ICD-9-CM. Although there is probably more agreement between the two systems than disparity, there are differences that may very well effect that final codes listed or collected for reporting. A coder should always follow and be familiar with the rules and guidelines in ICD, as that's how he or she will report the the diagnoses.
ICD-9 establishes that secondary codes (e.g., those listed on Axis III) are only to be reported if they were treated, factored into medical decision making, observed, assessed or otherwise monitored. That rule would distinguish what (if anything) is coded off Axis III. Psychiatrists do not always treat chronic conditions like COPD, hyperlipidemia and CAD. Those would be collected on Axis III, but it'd be up to the coder (and possibly the provider in query situations) to establish that those were actually relevent to the encounter.
Good luck to you. I wrote an article on this topic in September, 2007 Coding Edge. You may want to read that for any clarification.