The skuls can be used to denote command squads, or can just be used as random insignia. the other markings are supposed to be campaign or army markings and can be used to tie together a numebr of different units with a common insignia.
Regarding the numbers, it supposed to represent company, platoon and squad numbers. So 541 denotes 5th company, 4th platoon, 1st squad. A 0 can also mean a command squad or another squad not in the regular organisation path, so 609 is the 9th squad attached to the 6th company, but isn't in any of the line platoons. It could be used for heavy weapon or special weapons quads, or a
CCS.
Or you can come up with your own ideas for what the designations mean