We get questions like this (or tangentially related) pretty frequently. So much so that we're considering making this much easier.
In the meantime the way to do this (as of wyBuild 2.6.18) is to deliver the appropriate wyserver.wys file to the user depending on what version you want them to have. This means 2 things. First it means you'll have to keep all your old updates on your sever. And it also means you have to programmatically deliver the *.wys file the customer wants.
You can use the example code in the Limit updates article to learn how to deliver the version the customer needs based on inputs.
Tell me if this helps.
Also, for the initial install I am using click-once, not a traditional setup.exe/msi installer. So the very first time someone installs they use click-once, then all subsequent updates are controlled via wyBuild since click-once is not as controllable.
Is there any reason in particular you're using ClickOnce for the initial install? I ask because we're releasing installer-building functionality in wyBuild 2.7.0 and we don't want to miss anything crucial.