When we've chained patches into an install we used msiexec.exe /i myfile.msi TRANSFORMS=mytrans.mst /p thepatch.msp /qb-! REBOOT=ReallySuppress
As far as I remember, this worked fine. The other option would be to wrap the install with a script and dynamically determine the full path to the MSI, MSP and MST files and insert those on the command line. You can get the source dir (sScriptDir in my example) like this:
Dim oFSO, sScriptDir
Set oFSO = CreateObject("Scripting.FileSystemObject")
sScriptDir = oFSO.GetParentFolderName(WScript.ScriptFullName)
If Right(sScriptDir,1) <> "\" Then sScriptDir = sScriptDir & "\"