Alternative to Google Earth to edit and organize KML files
KML (Keyhole Markup Language) uses a tag-based structure based on the XML standard. The developer page on google has some really good info on the structure of how the KML files are set up.
Here is a link to the Developer page: https://developers.google.com/kml/documentation/kml_tut
You can edit KML files in a notepad editor, such as Notepad++ or Sublime Text. This can allow you to rearrange folders, and change layer order.
The folders use the XML tag "Folder", and items inside the folder can be "Placemarks", "Document", "GroundOverlay" and others.
By editing the file in a text editor, you can change the properties for each individual feature.
Here is an example KML layout:
<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="http://www.opengis.net/kml/2.2">
<Document>
<name>Paths</name>
<description>Examples of paths. Note that the tessellate tag is by default
set to 0. If you want to create tessellated lines, they must be authored
(or edited) directly in KML.</description>
<Style id="yellowLineGreenPoly">
<LineStyle>
<color>7f00ffff</color>
<width>4</width>
</LineStyle>
<PolyStyle>
<color>7f00ff00</color>
</PolyStyle>
</Style>
<Folder>
<Placemark>
<name>Absolute Extruded</name>
<description>Transparent green wall with yellow outlines</description>
<styleUrl>#yellowLineGreenPoly</styleUrl>
<LineString>
<extrude>1</extrude>
<tessellate>1</tessellate>
<altitudeMode>absolute</altitudeMode>
<coordinates> -112.2550785337791,36.07954952145647,2357
-112.2549277039738,36.08117083492122,2357
-112.2552505069063,36.08260761307279,2357
-112.2564540158376,36.08395660588506,2357
</coordinates>
</LineString>
</Placemark>
</Folder>
</Document>
</kml>
Check out an iOS app called Map Plus
I used it to create a bunch of polylines from road directions. I'm actually researching what I can do with my data (specifically visualization) after exporting to KML