You can use the -server argument in tandem with the -updatepath argument. The -server commandline switch simply points to an alternative location to download the *.wys file. The *.wys file still contains all the update sites listed in your wyBuild project file.
To specify alternative download sites use the %updatepath% variable and the -updatepath commaneline switch. I.e.
%updatepath%/%file%
then
wyUpdate.exe -updatepath="http://example.com"