If I understand you correctly, you want to do a copy of one file if you're installing on x86 and different file (with the same name) if you're installing on a x64 platform.
First of all, you cannot create one MSI for 2 different platforms, since a x64 MSI simply will not run on a x86 platform and a x86 MSI will be installed using WOW64 on a x64 platform.
On the other hand, you CAN create one x86 MSI that contains 2 different versions of a file and selectively copy the appropiate file during installation.
The easiest way is using WIX (V3) instead of the build-in VS2008 MSI generator. WIX gives you far greater control over what gets installed on the customer's machine and where, the ability to generate different installers for different platforms and full MSBuild support as an added bonus. (see http://wix.sourceforge.net for more info.)
In case if you're wondering that WIX is still in Beta, the generated MSI files are perfectly OK and I never ran into a bug yet. (And I develop setup projects for a living.)
Finally, you can check with the VersionNT64 property if an x86 installer is running on a x64 platform. If that property is present, you're running x64, otherwise you're running on a x86.
Hope this helps.
I am fine with Vista 64 bits for .net and php.
A lot of conversation about it are already on SO. Here is some important point your might take in consideration for .Net:
You can develop for X86 on your new X64 machine without problem.
For PHP XAMPP work fine, Eclipse work fine too.
Best Answer
There is no x64 version of Visual Studio 2008. I'm running the standard 32-bit version on Vista x64 Ultimate and it works fine. There really are no day-to-day issues that I've run across. You just install it and go.