If you want to throw a check on whether to drop or run a file you can also throw a check on the call.
Check: IsWin64;
or even
Check: "not IsWin64";
This allows a quick and easy way to compile 32-bit & 64-bit application installers into one package, but only run the specific one.
EDIT: To expand a little further for those that might be searching for this, I wanted to follow up.
For example, if you want to only allow certain files to be copied down by the installer you could do the following:
[Files]
Source: "MyProg-x64.exe"; DestDir: "{app}"; Check: IsWin64;
Source: "MyProg-x86.exe"; DestDir: "{app}"; Check: "not IsWin64";
Adapted from source: http://www.jrsoftware.org/ishelp/index.php?topic=scriptcheck
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