You can customize the resultant executable installer either by providing your own scripts that the existing templates includes, or you can provide your own templates.
Of these, the easiest is to provide your own scripts to supplement the default templates. The most complex is to provide your own custom templates.
No matter which way you decide to customize the installation process, you will need to be familiar with NSIS and have easy access to the NSIS Docs.
We've also found the HM NIS EDIT tool, which is a free NSIS Editor/IDE, very useful.
The plugin provides two templates by default:
project.jelly to get access to information in
project.xml from within NSIS scripts.
setup.jelly which generates the final script for NSIS
compilation.