Load the solution file in Visual Studio:
Customize it and build it.
(This bits optional but recommended)
In the same folder as the SLN file create a file called publish.bat and put the following text in it
rmdir /S /Q LinqToXsd
copy .\Cmdline\bin\Debug\*.* .\LinqToXsd\
copy .\XOTask\bin\Debug\*.* .\LinqToXsd\
copy .\XObjects_NETCF\bin\Debug\*.* .\LinqToXsd\
This dumps everything needed to actually use your custom Linq2Xsd in a folder that you can copy into the solutions that will use them.
What customizations are you planning to write? :)