Window-based provides you with the most flexibility, and is probably what you want to choose after you've got a couple of projects under your belt. I find with the other templates that I'm usually removing too much code, and it would be quicker to just start from scratch.
I usually setup my projects by creating 4 subfolders under Classes: "Views", "View Controllers", "Model Objects" and "Helpers". Model objects contains all the basic object types, where as Helpers contains things like utility classes or similar. Sometimes, where relevant, I will also create a Table Cells folder underneath both Views and View Controllers. I move MainWindow.xib to the Views folder.
If the project is large, I will sometimes also have sub-folders for the Views and View Controllers based on the UITabBarController tabs. So if I have 5 tabs, then the Views folder will have 5 sub-folders, as will the View Controllers folder. I find this helps to keep everything logically together in the same place.
One other thing I do is create an Images folder under Resources, otherwise that folder gets way too cluttered very quickly.