Well, there weren't that many directories on the 32-bit setup. Don't let it make you nervous. They simply split out the "main" Program Files, for 64-bit software on your 64-bit system, from a second one for older, 32-bit applications. The (x86) version is unique to a 64-bit OS. Each of the Program Files trees has its own Common Files subdirectory, where installation procedures place files that may be shared with other applications. As I wrote above, "Program installation _usually_ makes entries into the registry and may write files into the Windows directory tree. "
Now comes a great deal of unasked-for advice, based on my very successful experience. You will have to re-install all your apps and games for a rebuild anyway, so having them safe on a separate partition will do you no good.
First, expand that OS partition and install all of your applications into a single OS partition. It's simpler, and it will make something I will write later easier. To do this, first make a system backup so that you can recover if my advice breaks your drive. Then use a decent partition tool to enlarge the OS partition to a nice, comfortable size. This can also be done, with some effort, with Disk Manager in Windows. Or a clean install into a larger partition.
Second, have two or more external or removable drives on hand. I personally have an antistatic case with ten bare drives, four more stacked on my desk (for casual experiments), and two of these:
http://kingwin.com/products/cate/mobile/racks/kf_1000_bk.asp . Any of my bare drives can just be popped into a running system.
Third, have backup software that can backup and restore your system partition AND your boot sector and, in Win7, boot partition. This software should be bootable on its own. I have used Norton Ghost and EASEUS To-Do Backup, Clonezilla is free.
Back up your system as soon as possible, preferably after a fresh install. Number the backup. Keep at least four of your most recent backups. If you are ever hit by a virus or other glitch, restore your last backup and you go flying off as if it had never happened!
Because I keep my whole OS and only my OS in my OS partition, I actually restore backups pretty frequently. To install new software, I first reload the last backup, then apply all updates all over again, then install the new software, then backup. My system has been running for three years, but the elapsed time on my OS is probably a couple of months, since I set it back in time so frequently and never back it up without doing a restore / update / virus scan cycle first.
I really don't care if my OS gets busted - I boot from a thumb drive, restore one of the two identical copies of my last OS backup, and off I go. I take this to an extreme - during the installation process, when I do a build out, I back up every few hours. It's a pain, but if I get something wrong I don't uninstall and worry about registry bloat and leftover files and spyware.
OK, so I am a little extreme in my methods. But the basic advice of having a separate OS partition, and saved backups from your last known good state, will keep your OS protected and, if you restore often, keep bloat to a minimum. Just make sure that your restore procedure can restore the MBR and the Win7 boot partition (I back up the whole drive).