OK, so it sounds like you are going to attend the lead auditor course, this should give you an in-depth understanding of what the requirements of the standard are and enable you to determine whether an organisation meets those requirements by auditing them against it.
I suggest this is what you do to your own system - audit it against the requirements of ISO 9001:2008 and establish which elements meet the requirements and which don't - from there you can draw up an action plan which will identify which aspects of the system need changing and which are OK. You can then plan the work, including responsibilities and timescales and set to work.
When you have the system back in working order you can contact your CB (or another if you wish) and ask them to conduct the stage 1 audit, followed by the stage 2.
I suggest this is what you do to your own system - audit it against the requirements of ISO 9001:2008 and establish which elements meet the requirements and which don't - from there you can draw up an action plan which will identify which aspects of the system need changing and which are OK. You can then plan the work, including responsibilities and timescales and set to work.
When you have the system back in working order you can contact your CB (or another if you wish) and ask them to conduct the stage 1 audit, followed by the stage 2.