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Preferences / Display / Colors and Fonts, file display border (destination/off/source).
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Preferences / Display / Colors and Fonts, file display background, destination background. That lets you have different background colors for source/dest windows. There are also things in Preferences / Display / Options which let you fade-out certain colors in inactive windows as another visual cue.
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(Please split unrelated questions into separate threads; info on why here) You can change double-click behaviour under Settings -> File Types. Usually you'd adjust the All Files or All Folders types at the top. When editing a type, the mouse button behaviours are defined on the Events tab.