The organisation of gamemaker's interface and workflow is cleaner and better than Construct, IMO. You have sprites, objects and rooms - draw a sprite, assign it to an object, give the object actions and events, put it in a room, and hey presto - a game! Every component of the game is available in an organised tree structure on the left hand side - sprites, objects, rooms, fonts, sounds, backgrounds, timelines, paths and scripts.
How does that differ from having a layout, and inserting a sprite, then drawing an image into it?
Everything to do with an application is found in the Project tab on the ribbon, and settings can all be changed in application settings, also. I wouldn't call it 'spread all over the place', though if you do have a good idea on how we can make it more intuitive, we'll definitely consider it.