Unfortunately, I don't really know of any guides other than the wiki. I can attempt to explain some of it though.
By structure them into a creature, do you mean placing them into a creature? It's added through the [BODY] token, with the ID of the body parts being arguments of the tag. Just be sure that body parts are not out of order. By which I mean that body parts that rely on other parts are not listed before their 'anchor'. For example, having the eyes listed before the head. Otherwise the part will not be added to the creature.
Body plans can be used to add materials or tissues to a creature, place tissues in relation to one another, or place tissues onto body parts, which also decides layer order and tissue thickness. Adding tissues and materials are simple enough, though placing tissues on parts is a little more difficult.
Here is an example for putting two tissues on each your custom parts:
[BODY_DETAIL_PLAN:CLOCKWORK_LAYERS]
[BP_LAYERS:BY_CATEGORY:MODULE:ARG1:10:ARG2:25]
[BP_LAYERS:BY_CATEGORY:CLOCKWORK:ARG1:10:ARG2:25]
[BP_LAYERS:BY_CATEGORY:SENSOR:ARG1:10:ARG2:25]
ARG1, ARG2, etc. allow you to choose which tissue goes into the part when you are defining the tag within the creature. If you want, you can put the ID of a tissue instead of ARG#, to make the part always have that tissue when used, so long as the creature has that tissue within their definition.
Within the creature, the tag will look like [BODY_DETAIL_PLAN:CLOCKWORK_LAYERS], and you can add tissues after the tag to apply them to the parts. For example, it may look like this:
[BODY_DETAIL_PLAN:CLOCKWORK_LAYERS:CLOCKWORK:CASING]
So the first tissue, named clockwork here, will take the place as the innermost tissue as ARG1, and the casing will be the outer tissue as ARG2.
Tissues are easier. Just look at the pre-existing ones and at the wiki's
token page.