Hey Andreas,
Yes, this is possible.
First you'll need to add at least 2 download sites within wyBuild. You'll need to make a "Just an update site" type download site and a "Just a server site" type download site.
The "just an update site" should be something like:
%updatepath%/%file%
The "just a server site" can be your normal server location (e.g. http://yoursite.com/updates/%file% )
Now, you can use wyUpdate's 2 commandline switches, "-server" and "-updatepath":
wyUpdate.exe -updatepath="file://c:/temp/wyupdate-test/" -server="file://c:/temp/wyupdate-test/wyserver.wys"
In this example the server site location is overwritten with the location "file://c:/temp/wyupdate-test/wyserver.wys" and the %updatepath% variable is replaced with "file://c:/temp/wyupdate-test/".
To pass these along to wyUpdate from the AutomaticUpdater simply use the "wyUpdateCommandline" property.
Tell me if this helps.