Take the cover assemblies off of them IF you want to boil the bottles... Don't see a reason to boil the bottles though. Well, not if you use StarSan to sanitize them.
I use the Grolsch style bottles all the time. I never boil them (it would be a PITA to boil up 36 bottles, not to mention take a long time to go through them all), just use StarSan and a bottle tree. I leave the cap/tops on them so that they are also sanitized with the bottles. I have a spray bottle of sanitizer on hand, so I can give a quick spray of the tops of the bottles next in line for filling. No infections/problems to date using this method.