As soon as the installer has finished, you'll be asked if you want to run PiBakery. You can run it now if you want, or later from the Start Menu (or Desktop icon if you chose to have one).
The first time that PiBakery is run there is a small possibility that it may tell you that there is an update available. This update is optional and if you choose not to update, you'll be asked again the next PiBakery starts.
And that's it! PiBakery is ready for you to use!