Look at the BARF forum, and look at the menu's thread. There is so much information on how to get started. The bones don't puncture because they are softer and get digested. They would of they were cooked because the composition of the bone has completely changed.
You have to have the right balance of bone, MM, and organs.. too much or too little of one or the other may cause the issues you are seeing. Look at threads this sub-forum it's really really helpful and has links to many different sites.
I used to do raw and buy everything and portion out. Now I do kibble in the morning and a premade raw at night that is portioned for me.. I'm lazy like that though