You can edit .pro file in your wizard. The wizard files are in the following directory:
Qt-Dir/Tools/QtCreator/share/qtcreator/templates/wizards/
If you look at the directory there are some folders related to different wizards. For example if you look in to the "helloworld/qmake" folder, there you can see a "project.pro" file and a "wizard_sample.xml" file. You can edit the xml file to have your custom wizard.
"project.pro" is a template pro file. You can edit it and next time you create a project by that wizard, your custom pro would be created for the project.