Semi Zombie thread.
I just received a Soundcraft Signature 12 from Sweetwater and am enjoying it so far. But one thing i don't understand is that i'm able to adjust panning in my monitors but the headphone mix is all mono with the panning controls having no bearing on the routes. Any thoughts on how to correct?

Are you using SOLO, Solo is Mono, The main output without SOLO enraged should be stereo. 
Study the owners manual for detail of how routing works. 

Thanks I've been working with it for about a week and have a beginning understanding of the routing and that's making things a lot easier. Managed to figure out the headphone mix as well.
 
I have noticed the input signal into the DAW is very low and wondering if that's something I can adjust. I know it's ok in a digital environment but seems strange. I'm tracking bedroom level guitar through a cloudlifter into the Sig12 and I have to crank both the pre and the fader to get any kind of readable signal.

Cloudlifter makes DI boxes is that what your using? You possibly have a impedance miss match. 
If it is a cloudlifter mike then I guess it's a wimpy output. 
Generally my benchmark is a Shure SM 58 is almost always requiring the gain to be set at around 1 o clock on just about every mixer I've ever owned. 

I'm using a SM57 into a Cloudlifter CL1 into the SIG12.
I'll have to do some experimenting with looping the source and trying with and without CL, other mics etc. Will update!

Why do you have the cloudlifter in the signal chain? 
Your running a pre amp into a pre amp,,,That should actually make it way to loud, but there's no benefit in having it there. It is a device used when you only have a line level input. One of the Soundcrafts better attributes is it's pre amps are considered very good quality for the price point. 
So a SM 57 plugged in directly will give you what your after. Your gain will most likely be set at around 1 o clock. Sing real loud into the mike and turn the gain up until the peak light comes on then back it off a bit. 

I put the Cloudlifter in because I'm doing low volume recording and I can get a good signal without cranking pres too high. I'm hearing a strong signal in the mixer just the wav form in the DAW is very very minimal.

I just started using my MTK12 a few weeks ago with SONAR. Both impress me, easy to use together as a home project studio. My mic recorded waveforms were small,too,compared to the stereo .wav file I added to use as a drum/backing track, which showed up the same original size in 3 different DAW's track windows. That was with a strong,peak signal going in, no reason to have small wave forms in the recorded mic/inst channels. Did the same in Studio One 3.5. I will be able to get back to recording this week and see what the heck that was all about. 

Yes I've also got existing wav forms from the projects that I recorded using a Line 6 interface.
I'm wondering if it's a routing issue:
Mic > track 2 > Master
I wonder if it should route:
Mic > Track 2 > Track 3 > Master.
Then maybe you can adjust the gain on the Track 3 input.
Still need to experiment i guess and RTFM

What does the track meter show? 
Generally Sonars meters will show approximately what your interfaces meters are showing. 
It's possible they have purposely padded down the USB output so as not to go over during live recordings where the live sound might be on the edge of clipping. 
 
If the mixers peak light is active , but Sonars track meter is way down then that's proof. No big deal, it's digital so you can apply normalizing to bring it up to par. 
 
What you need to keep in mind is this is a Live Mixer first and an Audio interface second. It's optimized for live not recording. The recording feature is an add on to help sell the board to bands wishing a rough live recording of gigs. It is why I might be purchasing one. I'm not going to even dream it will replace a proper interface,, even though that would sort of be nice.