Hang on... A few points:
1.) It will still put some items into an x86 folder for backwards compatability and x86 modes of apps.. no worries
2.) With 2008 there are not separate ISOs, it is aware of your OS level. As long as you have an x64 OS you should end up with the right SQL installation. You are fine. You can verify afterwards but nothing you have said scares me on your behalf.