Navigation isn't a problem, it's that I have no idea what I'm navigating towards...
Being able to flick between files at will does help with learning what you need to be looking for, because you can easily check bits of the raws against each other and follow creatures from their entry back to their templates.
Relevant files, from raw material to creature, are:
material_template_default, for the physical stuff the creature is made of.
tissue_template_default, for each tissue type the creature has.
b_detail_plan_default, for weaving the previous two items into templates that can be called on by any creature. Some of these take arguments from a creature entry instead of being complete when called. Since the file is a collection of commands instead of a collection of things, it's... I dunno, more varied at first appearance than the other creature-making files? I found it the hardest thing to grasp, anyway.
body_default, for the parts named in the [BODY:whatever] part of the creature.
creature_whatever, for assembling all the above stuff.
You don't necessarily need anything but the creature file for quite a lot of things (see iron men for an example), but it's easier to note what you want and then go back to the two template files to start making it. Plus, that way it can be used by another creature.
The main thing that bothers me is that you can't create new materials per-creature, only new tissues.
I've been fooling around with special templates that have no tags to tell the game what to do with them, only the information about strength and identification. This -
[CREATURE:INORGANIC]
[DESCRIPTION:Abomination!]
[NAME:crime against nature:crimes against nature:travesty of]
[DOES_NOT_EXIST]
[FANCIFUL]
[USE_MATERIAL_TEMPLATE:AMMONIUM_CHLORIDE:INORGANIC_BLANK_TEMPLATE_STR]
[STATE_COLOR:ALL:WHITE]
[STATE_NAME_ADJ:ALL_SOLID:ammonium chloride]
[STATE_NAME_ADJ:LIQUID:melted ammonium chloride]
[STATE_NAME_ADJ:GAS:boiling ammonium chloride]
[DISPLAY_COLOR:7:0:0]
[MATERIAL_VALUE:1]
[SPEC_HEAT:50]
[IGNITE_POINT:NONE]
[MELTING_POINT:NONE]
[BOILING_POINT:10608]
[SOLID_DENSITY:200]
[LIQUID_DENSITY:200]
[PREFIX:NONE]
[USE_MATERIAL_TEMPLATE:BENZENE:INORGANIC_BLANK_TEMPLATE_STR]
[STATE_COLOR:ALL:WHITE]
[STATE_NAME_ADJ:ALL_SOLID:frozen benzene]
[STATE_NAME_ADJ:LIQUID:benzene]
[STATE_NAME_ADJ:GAS:boiling benzene]
[DISPLAY_COLOR:7:0:0]
[MATERIAL_VALUE:1]
[SPEC_HEAT:50]
[IGNITE_POINT:11008]
[MELTING_POINT:10009]
[BOILING_POINT:10144]
[SOLID_DENSITY:200]
[LIQUID_DENSITY:200]
[PREFIX:NONE]
and so on
- doesn't produce any errors on opening Arena mode. Material reaction products can be left off a template and added directly to a creature entry. Removing [IS_METAL] from the metal template and adding it only to steel resulted in an embark with only steel anvils, picks, and axes available, so I'm guessing that anything in a material template is fair game in a creature entry calling that material template.
So even if you can't technically create new materials, you can alter an existing template to be several totally different things.