Security Templates

I am trying to secure a stand alone (not part of a domain) web server. I got the hisecweb template from Microsoft and made a few changes to it in the Security Configuration snap in. I applied the changes, and re-ran the analysis, everything looked good. I rebooted and it was clear that at least some of the changes I made took effect. My problem is when I look in Local Policy, or in GPEdit.msc, many of the changes do not show there. I went back to the Security Configuration and re-ran the analysis and it showed both the database setting, and the effective setting were what I wanted. My question is which one is correct? Are all my settings applied as desired?

As usual thanks for all help and suggestions.

Dan