Web parts can be used on both portal page templates and ASPX page templates. However, with ASPX page templates, you lose the friendly user interface and need to set the properties in Visual Studio.
Go to CMS Desk -> Content, click some page and choose Design in the toolbar. You will see the page template structure like this:
Every web part can be moved up/down, to another web part zone and it can be configured using the Configure () button. It opens the Web part properties dialog like this:
When you click OK, the changes are saved and the window closes. When you click Apply, the changes are saved, but you can continue modifying the properties. All changes are applied immediately, the page templates are not connected with workflow or versioning.
Impacts of changing page templates
When you change a re-usable page template that is used by several pages, the changes will appear on all page templates.
If you need to modify only a single page structure, you need to clone the page template as an ad-hoc template or as a new page template. See also Cloning and modifying a page template.