Short answer is - you can't create one install for both platforms. But you can condition components to only install on different architectures. Like using condition VersionNT64...
A single MSI can only target one platform, so if you want to support both installations that run on 32-bit platforms, and installations that install files or registry keys to 64-bit areas, you need two .msi files. In InstallShield 2012 Suite projects, however, you can combine multiple .msi files into a single installation experience. This may address your need.
If you create an installscript program you can use FeatureSelectItem to select and deselect 32 bit and 64 bit Features.
If you want to do it this way and need any help to structure your setup or write the code let me know and I will give you some worked exampoles of what we did.
