Sorry for the long delay on Cisco responding to this question. Unfortunately there is very little information to make suggestions on what you can do to address the issues you are encountering.
Q1. The method and tools for troubleshooting conference calls will depend on what type of conference bridge is being used (SW based or IOS based or Cat based). Troubleshooting will also depend on 'what' the problem is. Is the issue related to call setup, is it choppy voice, does everyone on the bridge have the problem, does every conference on the HW/SW resource have the problem? I am not aware of many tools available to troubleshoot conference bridges specifically.
Q2. Cisco has a product called Cisco Prime that does include Voice quality tools to help with a voice deployment. I do not know many details, but Cisco Prime is our network management tool that can help maintain voice deployments.
Q3. Again, Cisco Prime can help with isolating issues holistically, but when you need to troubleshoot specific gateways, then the IOS show and debug commands will help quite a bit with determining a problem.
Thanks,
Dan Keller
Technical Marketing Engineer