MSU Files are deployed with the "wusa.exe" command-line utility. The syntax is pretty simple, but falls outside the scope of what Patch Manager does by default. Someone might have a super-clever way to handle this within Patch Manager, but I haven't done it myself.
I had to do a similar thing for an Exchange 2010 preparation. I scripted it out as "C:\Windows\System32\wusa.exe <path to MSU file> /quiet [/norestart | /warnrestart | /promptrestart | /forcerestart] /log:C:\FullPath\To\LogFile.txt"
Within Patch Manager, you could "bundle" this with another unrelated patch and have the above executable run as part of the PackageBoot process.
Just my 2 cents. If someone else has something a little more integrated, please post it! Don't think that one voice is the be-all-end-all voice.
KMSigma's response will get you most of the way there. You can provide patch manager a dummy application which does nothing, include the msu as an additional file, and put the required install commands in package boot as a pre-install task. You can also package the msu into a self extracting zip which you feed patch manager as the installer exe and have a post installation task that runs the install command.