Hey John,
Cause if you think about it, you should build the client file before you build your main app, not after. I hope this makes sense, just something I was thinking about.
You can really do it either way. For instance, if you're building wyUpdate to include the latest client.wyc with your updates then you can include an "old" client.wyc file (that is, one that doesn't have the latest version number but does have the latest resources -- theme, languages, download site, etc.). When you include a client.wyc within your update in wyBuild then it ignores the version number embedded in the file but uses all the latest information inside the client.wyc.
And if you're not including the latest client.wyc with your updates (that is, you're just building wyUpdate to include with your latest installer) then you can build wyUpdate either before or after you build your updates.
That being said we're always thinking about ways to make this simpler and reducing the learning curve.