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.
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