This can be done very easily guys we actually have a KB for it:
912997 Frequently asked questions about the Windows Installer .msp files for Microsoft Dynamics GP
mbs.microsoft.com/.../KBDisplay.aspx
Q/A13
Q13: If I have a test server that has multiple installations of Microsoft Dynamics GP 9.0 or later versions, will the .MSP installation patch all the installations?
A13: Yes. If you run the .MSP installation, all Microsoft Dynamics GP installations will be patched. If you want to patch only one Microsoft Dynamics GP installation, follow these steps: 1. Click Start , click Run , type regedit , and then click OK .
2. Locate and then click the following registry subkey:
Microsoft Dynamics GP 9.0
32-bit enironment
HKEY_LOCAL_MACHINE\Software\Microsoft\Business Solutions\Great Plains
64-bit environment HKEY_LOCAL_MACHINE\Software\wow6432Node\Microsoft\Business Solutions\Great Plains
Microsoft Dynamics GP 10.0 and later versions
32-bit environment
HKEY_LOCAL_MACHINE\Software\Microsoft\Business Solutions\Great Plains\1033
64-bit environment
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Business Solutions\Great Plains\1033
3. Expand the folder for the instance of Microsoft Dynamics GP you want to patch.
Note The DEFAULT folder is for the default installation. The Inst01 folder is for the second instance of Microsoft Dynamics GP. For example, if you want to patch the second installation, expand the Inst01 folder.
4. Click the SETUP folder, double-click the Product Code, and then copy the code.
5. Exit Registry Editor.
6. Click Start , and then click Run .
7. To install the .MSP file, type the following, and then click OK :
C:\updatename.msp /n {E979C594-95F9-4E3A-985D-A1DFDF403227}
Note Replace "C:\updatename.msp" with the path to the .MSP file and the name of the .MSP patch file. Replace "{E979C594-95F9-4E3A-985D-A1DFDF403227}" with the Product Code the you copied in step 4.