DJM-909 Proper Setup advice requested

First off, as my first thread I am starting here, let me say HI to the collective and get on with the issue which I find rather annoying, yet comical, but first, I am a n00b to using time code. I have owned this for 2 weeks, just got around to setting up the second x1 to use a sample based trigger mechanism, and have had a lot of fun with it thus far, but what I got to work doesn't match what is described in the manual.. i'll explain further and would love to hear anyone advice or suggestions on an alternative setup. I already noticed that some effects native to the DJM-909 don't seem to translate when recording a mix.

Scenario.
OSX 10.6.6

(1)DJM-909 Mixer
(2) SL-1210M5G's
(2) X'1s
Audio 6 and Traktor Scratch Pro 2
2011 Macbook Pro 8gb ram


The mixer is monitoring through the two sets of master outputs, (2) KrK V8's out the XLR outputs and (2) KrK V'4s out the rca master outputs. The Output on the "Booth" is ran to the input 1+2 on the front of the Audio 6 and the output 1+2 on the Audio 6 are ran to the "session in" on the DJM-909 so all laptop sound runs through the mixer, otherwise monitored by headphones out the front of the Audio 6

Now here is the fun part. I called and spoke with a tech rep who had no idea what the DJM-909 was, and when i explained to him it was the same mixer used by craze in the promotional video I was told in a cocky tone that "oh, well im not into dj'ng so..." okayyy.. I wont go off on that issue and I understand it was 4:45 and the techy probably had a long day so to stay on topic in my own thread i'll just continue because I can go on forever about the importance of good customer service. Needless to say I have not called since, hence my participation here.

So the issue was what many seem to have, time code sound translating through their monitors. I realize the settings in the application play a major role in getting this system setup correct and while i have been able to record with minimal timecode sound (non existant audibly when the ruckus that is drum and bass is sounding out my monitors).

My question is this. The manual says use the Line/CD input on your mixer. Well the 909 has either:
1) CD
2) Phono/Line (with a switch on the back of the mixer that toggles between the two)

So far this is what I found to work best, and I THINK I have tried every possible combination but please suggest an alternative regardless if this incorrect.

I have the outputs for 3+4/5+6 on the Audio 6 going into the CD RCA inputs on the 909. On the Audio 6 software side of things, "Phono" is the option checked under the input. Both decks calibrate to Vinyl 10 with this arrangement and form a very close to perfect circle in the time code calibration section of the preferenes.

Does this setup givin the info provided sound correct? I am aware of the usb port issue with macbook pro's and am using the correct port. I just recorded using amedeus 1.5.5 and everything sounded good.. am I always going to hear the time code from the needle on the record even when the volume is turned off?

Lastly, givin this setup, or this mixer in a live gig setting, how would you go about playing a normal record without enabling the direct thru on the software? Is there a shortcut command that can be set on the X1? I followed the instructions on how to set up the second X1 as a track sampler and it states if you see (2) or more x1's in the list, reset the controllers and apply the patch and then you should see one X1 and one sample deck. However, I still saw two x'1's in the drop down menu along with a sample deck. Is this normal? According to the Knowledge Base I should only see one of each.. Thanks for any help anyone can provide. I tried to title this best I could. It's frustrating so many posts at this board that read "HELP!" with no reference point.. I hope theres a few 909 users here that can advise how to deal with the effects, ie, to route or just use as is..

Thanks!
HoH
c4rlo