I have an assembly with the following manifest embedded:
Instaed of relaying on side by side I would suggest you to don't include the "Manifest file" inside your assembly. Expecially because you cannot be sure that the PC you're going to install your software is updated to the version included in your manifest.
You can disable it setting the project property "Linker\Manifest File\Generate Manifest" to "No".
I hope this could help. Good luck