Hey Robbie,
Currently wyUpdate sees folders as either "completely in the user's control" or "may or may not be completely in the user's control". If the folder is in the "completely in the user's control" group (i.e. the %appdata% folder, the desktop, the my documents folder, etc., etc.) then wyUpdate won't ask for elevation.
But, if the folder being updates is in the "may or may not be completely in the user's control" group then wyUpdate will always ask for elevation.
We do plan to make wyUpdate more flexible out-of-the-box. In the meantime, you can modify wyUpdate to never elevate. Or better yet, modify wyUpdate to dynamically check if the current user has permission to install to a custom folder (and then submit the patch back to us so we can include it for everyone). The relevent bit of code is in the "frmMain.UserElevation.cs" file. Specifically the "bool OnlyUpdatingLocalUser()" function.