Yes, you do need separate MSI files for 32-bit and 64-bit, assuming that you have 64-code that you want to install and run. 32-bit apps will install on 64-bit systems and run in 32-bit mode, but it appears that you have 64-bit Dlls.
This is a good outline of why you need two installs:
https://blogs.msdn.microsoft.com/heaths/2008/01/15/different-packages-are-required-for-different-processor-architectures/
For example there are different folder locations such as ProgramFilesFolder for 32-bit program files and ProgramFiles64Folder for 64-bit setups.
and this link:
https://msdn.microsoft.com/en-us/library/windows/desktop/aa367451(v=vs.85).aspx
points out that 32-bit packages can contain only 32-bit components, and 64-bit packages can contain 64-bit and some 32 bit components.