This article describes how to package 64 bits applications using deployment manager.
Deployment manager is a 32 bits applications so it can't have access to the areas dedicated for 64 bits applications on a 64 bits machine. Eg. "C:\Program Files" or registry entries under "HKEY_LOCAL_MACHINE\SOFTWARE".
There is no special requirement for packaging 64 bits MSI applications as deployment manager can read the MSI database on a 64 bits machine regardless the MSI application is 32 bits or 64 bits.
To package a 64 bits third party installer package, for step "Package install and uninstall keys" in the packaging wizard, under "Specify a unique value created by this package during installation that can be used by the installation agent to determine whether this third-party installer executable should be invoked", please enter the registry key under an area the 32 bits installation agent can read. For example, the key can be under "<HKLM>\Software\Wow6432Node", but can't be under "<HKLM>\Software" as the 32 bits installation agent can only read the registries under "<HKLM>\Software\Wow6432Node".
Similar reason to the above, the installation agent can't read or create a file under "C:\Program Files". But it can access to files under C:\Program File (x86).