what i do is put a secondary folder within the primary one
env/env/(i tend to move these into the textures folder and repath the scripts)
scripts/scripts/mapname.script and mapname.arena
maps/maps/mapname.map mapname.bsp and mapname.aas
textures/textures/mapname/textures...jpg and tga
etc..
and then paste the current files into it, drag and drop into the zip
i keep all the files in folders within the mains though

im for the idea of a contest naming convention though for differentiation of these maps within the folder system for those of us who extract the pk3's also id like to see the .map file included for all maps.