Hi Tim,
You can use Settings > Default to get the default settings Skyline uses when you first install it.
If I were trying to figure out what was different in the settings of two files, I might consider saving and exporting two settings files (.skys) and then using a visual diff tool like WinMerge or TortoiseMerge to see how the XML text differs between the two. You can use Settings > Save Current to save the settings of any document you like, and then Settings > Share to save a .skys file, which will express the settings in XML text.
There is not a way to put either the peak height or peak area text on the chromatogram graph. The best way to get access to the exact values would be the Results Grid.
Thanks for using Skyline.
--Brendan