It really depends on what you are trying to debug. The debug pkt commands are very useful, but on the other hand it's just a packet dump for any packet with a mac address that matches the filter you configure. That might be ok, if you trying to figure if packet is sent/received from the AP, but if you are having trouble with say keying or something like that, you might not really get much insight.
With regard to the second part of your question, you need to run the debug on local IAPs. Now, there are situations whereby some traffic is sent to the master e.g. if you're using an IAP-VPN and it's NOT per-IAP tunneling. In those cases, you might have to run the pkt debug on both a local and master IAP.
Is there a specific issue / behavior / symptom that you're trying to troubleshoot?