Textures should be in textures/<mapname>/; for example if you take a texture from map-atcs-1.1.0.pk3/textures/atcs/ you should put it in map-mymap-version.pk3/textures/atcs/. Tho generally, you don't need to include textures from default maps. However, if you edit a file taken from another map, do NOT put it in the same folder, instead put it in map-mymap-version.pk3/textures/mymap/ for example.