There are two different layers you're working there.
clock source line refers to the synchronization of bits in the layer 1 and layer 2 level. This is a generic T1-level configuration. You would use this for many different types of T1 connections.
The 'isdn protocol-emulate network' decides which side is going to be the Q.931 network or user side switch. This enables a different type of Q.921 and Q.931 messaging between the device. This configuration is specific to PRI's.
These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...