Firstly, you need to understand difference between webparts/widgets/ascx user controls/transformations and other entities)
Webparts are Kentico components base on acsx control or another webpart which you place in template
Widgets are Kentico components too, but they are base on webparts and they have another purpose
Transformations are code templates that determine how listing web parts and controls render content (in general)
Usually we use Portal Engine development model (it has its own advantages and disadvantages), it means we don't have any aspx pages. All templates we store in Kentico. And we create custom webparts for these templates with our own HTML markup.