I've had a bad time connecting my deck, and so I'd like to step back and take things slower - so here's my first question I need to sort out.
On my timeline, there is the DNA/1394 button, and I get very different results depending on which way it is set.  I'm looking to determine which is right for me (and perhaps I'm not even understanding its purpose), so here's my info:
Xpress DV PRO with MOJO running firewire to a Sony DSR-2000 deck for video, and using a 9-pin serial cable for control.

My symptoms:
When I have the button set to DNA, I can view output on my external monitor, but cannot capture. I cannot see video when capturing - just a black box and I get: Error -"Audio/Video is unexpectedly not available" or something similar.  I do have deck control.
When I am set to 1394, I get the error "No input signal present" and I have no monitor output. I have deck control this way too. 

I set up my deck on one channel - Direct - Com1
When I set up my deck as Firewire - DNA, then I can capture video just fine, however only when my deck is set to iLink. When my deck is set to 9-pin, I lose control.

So basically, I'm stuck. Either I can capture video, OR control the deck depending on how I set up my deck. Some have suggested that I use 2 channels - 2 deck setups, however I don't see how this will help. It seems that I should only have 1 deck setup since I'm only using one deck.

So, with my setup of a MOJO, and 9-pin control desired, which way should my DNA/1394 button be set?  Thanks to all.

When you have the DNA button selected, your audio and video is going through your Mojo.  When you have 1394 selected, the Mojo is being bypassed and video in/out is going through the firewire port.

If you have 1394 selected and deck is set up Firewire on OHCI then you want the deck set to iLink and you will be using the firewire for deck control and audio/video input and output.

If you are using the Mojo you would configure the deck as Firewire on DNA and use the iLink deck control.  I haven't had much luck using 9 pin for deck control and firewire for audio and video with avids.  If you want to use 9 pin you should probably use Component video.

Keep in mind that you can only do dv25 over firewire through the mojo so if you are doing dv50 or something it will not work.  If you want to use firewire for capture you might as well go direct to your firewire card because there is no advantage of going through the Mojo for capture

I'm confused here:
"When you have the DNA button selected, your audio and video is going through your Mojo.  When you have 1394 selected, the Mojo is being bypassed and video in/out is going through the firewire port." 
Okay, but my video is BOTH going through my mojo and firewire. I'm running firewire from computer to mojo - firewire from mojo to deck.  Is this not correct?  I am determined to use the 9-pin and non-analog video, since that is the only way to be frame accurate and not lose quality - both are absolute requirements for anyone working in video production. So, I think the iLink control is out as well as the option of going Component.  I'm using DV25

When you select the 1394 button , it is essentially like the Mojo is dissconnected from the computer.

So what you want to do is keep DNA selected in your timeline.  Connect the deck by 9pin and firwire from the deck to the Mojo.  Set up deck configuration as Direct on Comm1-DSR2000 and set your video input tool to DV and try capturing. 

If you get an error, post the exact error message. 

Firstly, thank you so much for your helpful explaination - I think some real progress has been made here thanks to you.  Ok, when I'm setup as you say, my deck control is great, however I cannot see video in the AVID - no preview while capturing, just black boxes.  Then, when done capturing, the process aborts and states, "Exception: Audio/video is unexpectedly no longer coming into the system."  I've done a few searches on this phrase, with limited success, however.

I'm going to go reinstall the mojo driver and see if that helps first.

UPDATE:  Things seem to be working now - the reason?  My deck has a setting called "SDTi/iLink" - I assumed that since I'm using firewire to transfer video and audio data, that I should set this to iLink, however if I switch to either V:SDTI or SDTI for this setting, it works.  Huh.  I have no idea what this setting does except cause me confusion.  But hopefully this is the answer!  Thanks Ravidedit!!! I really appreiate your wisdom!