Do you mean the Farm Configuiration Wizard in Central Admin?
The general consensus on the FCW is, use it very sparingly. It's fine if you want a quick overview of SharePoint or you are setting up a non-specific Dev workstation. The Wizard uses a bunch of default settings that go against most enterprise best practices, most notably using the same accounts everywhere and randomly-named databases. Also as you have found out, it's pretty obscure what exactly it is doing with your farm.
See for example these articles: Link 1, Link 2
For a controlled, repeatable installation you can look into the AutoSPInstaller Project on Codeplex
If you want to set up the services with the same information, you can look through Central Admin on your production farm and write down the settings in AutoSPInstaller's config files, so you'll have a reusable template. Some of the more obscure settings might need to be fetched with Powershell.