The next bit that we need to do is add the files that comprise our application to the eventual installation directory, along with anything else that we want to add, and then create some shortcuts. This is all very straightforward so I'll just show you what the files and folders screen looks like.

All that I'll mention here is that the updater.exe and updater.ini files relate to my desire to ensure that this application can automatically update itself when a new version is available, and the TbExample.aip file is simply the project file created by Advanced Installer so that you can see for yourself what This installation project looks like.
Your application probably doesn't need any registry settings per see (and any that the ToolBook Runtime need will have been taken care of by the Neuron installer.) However I do want to provide the ability for the application to automatically update itself when I have a new update available and I'm going to base those updates on program version numbers. Those will need to be checked prior to an update and the best place to do that checking is within the registry. I need the check to be machine wide so that means that any change I make needs to be to the HKEY Local Machine hive. Here you can see how I have done that on the registry settings page.

With our registry entry taken care of we now turn our attention to the media section. Here you can make all sorts of decisions about how your installation will be packaged. In this instance as the Neuron installer is not that big and my application itself is tiny it makes more sense to wrap everything up into a single file.
When we originally chose to add a prerequisite piece of software (the Neuron Installer) to our application Advanced Installer automatically created a .exe setup file. Ordinarily the application msi would be packaged next to this (along with an autorun.inf file if we wanted one created. However my choice in this instance is to wrap everything into a single file so you'll see in the 'Package' section on the 'Bootstrapper' tab I have selected 'Include install files in Exe' and in the MSI section we have 'Included in EXE Bootstrapper' selected.