So i finally broke down and signed up to this forum to get some help. While exploring I found the files section and found this deep dive training presentation. http://e2e.ti.com/support/low_power_rf/m/videos__files/653593.aspx
I'm not sure if you can get to this without being signed in, but really wish I had found it weeks ago!!! This breaks down the protocol, hardware, and software. Explains clearly and simply the setup of new profiles and how to interface with the firmware. This should be front and center as the default reference material in the documents section of the CC2540 web page!
Maybe if enough people request they will help us newbies out! At least tell people that more in depth material is available if you sign into the community!
Cheers!
Marty