I am looking for some tips on how to best organize Policies, Rule Modules and Rules.
Specifically is it better to create more Policies, Rule Modules or Rules.
Leave as much of the original configuration intact as you can and make new policies>modules>rules for your exceptions.
This will not only make it easier to manage, it will make upgrades much easier.
Upgrades will replace original configuration objects only if they have not changed.
The more that are replaced by an upgrade, the less you have to do manually.
Having all exceptions in a single policy or policies should allow you to manage them more efficiently too.