If you use the Mapper 2.0 (in the Utilities section of the Downloads), you have the option to split the map based on the height value. That will group lines together to make it easy to delete one set or another. Inkscape also offers some rudimentry Layers support. I tipically use the split feature of Mapper 2.0 and then raise/lower the sections into layers.
This does have the advantage of allowing you to make maps that line up, so long as you keep the seperate top/bottom images centered when you shink 'em down for the photoshopping.
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