You use an <exclude_gpu> in your cc_config file. It allows you to prevent a gpu from being used by a particular project. Its a client side things, doesn't require any change on the server.

My cc_config file:

<cc_config>
    <options>
	<http_1_0>1</http_1_0>
	<http_transfer_timeout>120</http_transfer_timeout>
        <exclude_gpu>
            <url>http://climateprediction.net</url>
        </exclude_gpu>
        <exclude_gpu>
            <url>http://einstein.phys.uwm.edu</url>
        </exclude_gpu>
    </options>
    <log_flags>
        <sched_op_debug>1</sched_op_debug>
        <work_fetch_debug>0</work_fetch_debug>
    </log_flags>
</cc_config>

You can see I have excluded my one and only GPU from being used by both Climate Prediction and Einstein. This particular machine uses the GPU for GPUgrid work. You can have multiple <exclude_gpu> statements.

If you don't already have a cc_config.xml file you'll need to create it in the BOINC data directory. Use a text editor such as Notepad and make sure its an .xml file (notepad likes to put .txt on the end of the file names). After doing this either re-read the config file (on the menu bar Advanced -> Read config file) or shut it down and start it up again.

Details about the config file can be found here