NOTE: I'm not a moderator or member of wyDay.
However, maybe this helps:
You put your app files some arbitrary place, unrelated to where they will be installed, and unrelated to your FTP server.
For example:
S:\Development\Our Product\1.0S:\Development\Our Product\1.1S:\Development\Our Product\1.2...
Each time you make a new version, you create a full copy with changes in a new location (1.1, 1.2, 1.3, etc.).
Your wyBuild stuff you keep elsewhere, e.g.:
S:\Development\wyBuild\Our Product\Our Product.wyp
When you add a version to your .wyp, you add the files/folder above (so 1.0 refers to S:\Development\Our Product\1.0, and when you add 1.1 to your project, you tell it to add the files & folder from S:\Development\Our Product\1.1, etc.)
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Separately from all this, when you install your software, you keep using the same location for all versions:
C:\Program Files\Corporation\Our Product **
That location gets a copy of the current wyUpdate.exe and client file.
Then you can run wyUpdate.exe in the install location (C:\Program Files\Corporation\Our Product), and it will use the client file to know what version it is, and where on the FTP server to find updates.
Each time it pulls down updates, it updates the files in situ (i.e. C:\Program Files\Corporation\Our Product)
** NOTE: the installation location can vary from PC to PC - it has no meaning other than that your installer, that initially loaded your software onto the PC, include the wyUpdate.exe and .wyc files in the base installation folder. This location is never used by your wyBuild project, ever.
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Your FTP Updates location is arbitrary, but consistent. e.g.
ftp://myserver/updates/our_product
Each time you add a version to your wyBuild project, it uploads the needed deltas to this same location. Then when an installed copy of your software looks to see what's current, it looks in the same location always, and grabs the current from_current_to_target_version files.
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I hope that this helps.