There is a detailed answer from Rahul on StackOverflow about this that I wanted to highlight by blogging about it.
There is also one thing to add to it.
The Design Automation engines do not support having dlls and other resources for multiple versions in the same app bundle - you cannot rely on the PackageContents.xml file to specify which files should be used by which engine version.
If you need to use different dlls and other resources for different engine versions, then you should create a separate app bundle (or app bundle version) for each engine version that you want to support, and a separate activity (or activity version) that is referencing the correct app bundle version - as discussed in the StackOverflow answer.