...Next you have the tissue layers which define where each tissue goes, unfortunately I don't know too much about those yet so I can't really explain them to you...
The tissue layers from the body detail plan is where you actually assign the tissue material to the defined body parts. Using the [BODY_DETAIL_PLAN:(whatever)_TISSUE_LAYERS] template in the body_detail_plan file you associate each body part name (i.e. SKIN, HAIR, HORN] with an argument (ARG1, ARG4, etc) or a straight up value that was defined in the TISSUE_MATERIAL template (i.e. CHITIN, SKIN, etc). Like EYE in the vertibrate_tissue_layers it says EYE:EYE:100 that means EYE body parts are made of EYE material 100% of the way through, and TUSK:IVORY:100 means that any body part that is a TUSK is 100% IVORY.
The ARG# entries are defined in the creature file using a:
[BODY_DETAIL_PLAN:(whatever)_TISSUE_LAYERS:ARG1:ARG2:ARG3:ARG4...etc].
Inside the tissue layers template, let's use the same one vertibrate_tissue_layers, it says that BEAK:ARG4:100 so whatever material was fourth in the list on that line would be the material of the creature's beak. The usual values for vertibrate layers is:
[BODY_DETAIL_PLAN:VERTEBRATE_TISSUE_LAYERS:SKIN:FAT:MUSCLE:BONE:CARTILAGE]
so the BEAK would be all BONE.
And also from that same template, let's look at TAIL:ARG4:25:ARG3:25:ARG2:5:ARG1:1
This line means that the creature's TAIL (or tails) is/are 25 parts BONE (ARG4), 25 parts MUSCLE (ARG3), 5 parts FAT (ARG2) and 1 part SKIN (ARG1), and have no cartilage in them.
Joint templates add 'shoulder' and 'wrist' etc bodyparts that have the tendons and ligaments in them. If joints aren't added, the tendon and ligaments connect separate bodyparts directly (I think).