Where is it that you are seeing this problem with the quotes? The code on the page should look like this:
<?php if(!WA_Auth_RulePasses("Logged in to clients")){ // Begin Show Region ?>
this is something
<?php } // End Show Region ?>
In design view you should see the content of your show region with a thin box around it that has a show region marker associated with it.
When I have my show region on the page I can edit it from the server behaviors tab of the application panel and it will reflect whatever rule I change it to without encoding any quotes. Please let us know where you are experiencing this and exactly how you got it this was so that we can check this out further.