I never use the -projectdir parameter,
What I did was create a thinstall folder in the bin folder of the package.
Then when you have altered the package and the Thinstall folder is filled with the changes you browse via command prompt to the root of the package folder.
Start sbmerge: "C:\program files\vmware\VMware ThinApp\sbmerge.exe" print (to check if it can read the changes.
after you see the changes you can enter the same command but then with Apply behind it.
All changes are now entered in the package and only a Build.bat is needed to repackage.
This has been the way I've done it. I included a screenshot of a manual I was wrote for a customer. perhaps it will help you