As of this version of the SDK, all files that are included as a module dependency in the manifest file must reside in the same directory as the manifest file when installed. Other that that, you are free to install files however you wish.
Under the registry key HKLM\Software\Qbik Software\WinGate\Packages you need to create a key which has the same name as the package UUID in your manifest file. e.g. HKLM\Software\Qbik Software\WinGate\Packages\{F83CE035-1BA1-4B8A-BAB3-81FC56BD33D9}
Under that UUID registry key needs to be a string value named Manifest whose data is the entire path to the manifest file. e.g. C:\Program Files (x86)\MyCompany\MyWinGatePlugin\MyPlugin.manifest.
NOTE: On 64 bit systems the actual WinGate key is HKLM\Software\Wow6432Node\Qbik Software\WinGate