The "squad markings" that are the force org chart icons are a Codex Astartes thing; during the Heresy you might find Ultramarines marked that way, but probably nobody else.
The small black and white hollow diamonds full of numbers on the Salamanders decal sheet are their unit patches;
http://www.bolterandchainsword.com/topic/309304-salamanders-cuneiform-code-cracked/ provides an overview of what it all means. The larger square diamonds are battle honors, I don't know if they have specific meanings. I'm pretty sure the Word Bearers
had their own battlefield-role icons (there's a picture in one of the books with a pauldron patch labeled "heavy support"), but I'm not entirely sure what they are.