I usually use my colors with the default settings that Eclipse provides, but I know many people who like alternatives for Eclipse (usually using a dark theme), so I decided to try ...
To change the default colors, there are several places that you should view in the window> settings menu:
General > Editors > Text Editors (to set the background color / selection color, etc. for all editors) General > Editors > Text Editors > Annotations (to set the colors for the occurrences highlight, tasks, etc.) Pydev > Editor (to set the pydev editor-related colors) General > Appearance > Colors an Fonts (to set what not available in the other places)
Now that you have set these colors correctly, one thing you really have to do is export the settings you just changed so that you can import them later.
To do this, go to the menu "File"> "Export"> "Settings" and export all the settings to a file, then open this file and delete all non-color settings (except for the export_file, which is required by Eclipse when importing) - note so that you can save other settings that you enter all the time too, and it would be easier to do this with a clean Eclipse installation only with what you want to configure (so that you don't have too many settings in this settings file).
You can later import these settings into Eclipse via File> Import> Preferences.
The dark theme settings I'm using give the result below (note that you may have to restart Eclipse so that the left ruler looks right):
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