As CaptDan said,
"Note: when using Input Bypass, NONE of the channels' EQ, Dynamics or FADER LEVELS are affecting the signal going to Sonar. In otherwords, it's a straight through process where nothing steps on or prints to the tracks."
Which means that assigning channels 1-24 to layer two really doesn't do anythiing for you, unless you assign those channels to busses, so,,,to keep layer two available for other input mixing, try this...
Go to routing page /output slot/slot 1 or 3 (for your FW) and assign M/L 1-24 to your FW. (this will be the uneffected signal going straight to Sonar)
Now go to routing/input and assign M/L 1-24 to CH 1-24 (first layer..this will be your FOH mix).
Now hit SEL on each channel and push the "STEREO" buss button so that it is lit for each channel.
With this setup, each input. 1-24, will split. One uneffected version will go into each track input into Sonar (given that that is setup proerly) and NONE of the EQ, Dynamics, FADER movements etc that you make for live sound will be "seen" in Sonar. The only thing that will be seen is the preamp level, up at the top of the board as the signal is still in analog form at this point.
The OTHER split signal WILL go through your EQ, Dynamics, Effects. and FADER movements for each channel, and then out the stereo Buss (mains) for FOH,
Now layer two is available for anything or nothing. You could even assign 8 more channels for 8 external preamp channels in the same way, for 25-32 over FW and 25-32 out to FOH with a mix.