techp,
Policy Management will only apply those objects (settings) which you define within the policy. Any other settings you've made outside of Policy will stay the same. For example, if you have a policy that devices the Agent > Set Credential but does not define the Agent Menu, the definition you've configured in Policy for the Set Credential will apply to the endpoint(s) where said policy is applied. However, the Agent Menu settings will remain just as they are.
I would recommend you review the tech jams that have been presented on Policy Management to get a better idea of how the module works and what to expect when using Policies to manage your endpoints. Recorded tech jam presentations are available for review here: www.kaseya.com/.../techjams.aspx. There have been two presentations on Policy - one in June 2012 and one just last week.