In the Event creation part of a layout, you can manually load an image using "AppPath +". For example, say I have a folder called 'Game' and have my .exe in there. I then create a sub-folder called 'images' and put a file called 'pic.png' in there. In the Event editor, I can manually load that image using "AppPath + images\pic.png". I don't have Construct in front of me right now so I can't give exact details, but that's basically how it works. The downside to doing it this way, though, is that once you go back to the Layout editor you can't just drag and align that image visually because the image is only loaded when the executable runs and gets to the event.
What is it that you're doing that you would need to manually reposition the image after it's loaded? If you gave more details on what you're trying to make there might be a solution to help you out.
And if you're taking about something common like replacing tiles or sprites within a game, then obviously the tiles or sprites would have to conform to your game specs before importing them or they wouldn't work. The objects that you've already put in the layout would still be in the same places... you're just loading different images to them. If they images don't fit then the game would look funny, sure... but that's the same for all games that let you replace sprites and such, it's not just a Construct thing.