as far as I know this should work in 2016 but I didn't test it by myself so far.
You can create two msi packages one for 32 and one for 64 bit and set the architecture to the correct one in the package. It's a new tab under "Install/Uninstall options". Then create a bundle and assign the two packages to the bundle. Then schedule the bundle and leave the rest to LANDESK...that's the theory...:-)
I usually solve this with a batch script. Detect the OS arch in the script then call the correct msi.
Thanks Christian, it worked!
I specified for each package its architecture and then I created the package bundle adding the two MSIs. The bundle manage the whole process and worked like a charm.