You will find many entries for the same programme in both. Internet Explorer 8 is an example. You can run either the 32 or 64 bit version. The only difference is that Adobe has not released a 64 bit version of Flash Player. Therefore, for the moment, the 32 bit version is better.
Programme files are 64 bit programmes. Programme Files (x86) are ones installed in 32 bit. They work ok. For example I have Photoshop CS5 which installs in both versions. Only the 32 bit version allows me to use the TWAIN scanner interface.I Have w7 64 bit.