my most complex texture (being or the ragnarok line) is about 500 megs, well over a hundred layers and just as many spline paths. i arange them in layersets each representing a section of a ship (usually one per each contiguous chunk of uv space).plus a number of backfill layers which mask out the unwrapped background layer when i have it enabled (so i can view the completed map without being thrown off by any contrast differences imposed by the unwrap). usually a solid fill layer and a number of airbrused layers (i usually use a two tone brush with some metalic like texture applied) for backfill. my sections are layed on top of this and make heavy use of vector shapes, spline paths, and layer effects, or recently layers with no effects and fancy patterns drawn by stroking spline paths with advanced brushs. another think i started to do is to have additional layer sets which overlay the completed map for shine and env maps. they are either transparent or are set to multiply or lighten (depending on how shiny i want everything). from there i can copy the whole image merged and paste into the shine map and the env in its alpha chanel. i also keep a seprate layer for glows, this way i can try different different glow intensities and colors, i usually set it as lighten for viewing and normal for copying into the finished glow map. by tweaking the blending options of glow/shine/env layers/sets (to a degree, its not exactly wysiwyg) i can aproximate what they will look like without seeing the texture on the model ingame. it works well enought that i usually dont need to go back and tweek the effects maps when i load it into the game for the first time.