First off, the breakout cable of the Inputs are automatic for the babyface. TotalMixFx is a monitor mixer, meaning that you can tell the signal that is coming in on the Inputs and the signal going on on the Outputs, including the Headphones connections. So, whatever is coming in for the signal strength on the Input is also can be seen probably on your DAW (digital audio workstation) I guess that is Logic Pro. I am using Windows 7, and Sonar, but relatively still the same.
You set the inputs in your DAW to the Babyface left, right, or stereo, depending. Usually you set up the drivers to use in the computer for ASIO drivers for the Babyface. That way you record and hear back at the same time (with Windows 7 drivers, there would be lag or latency in which case what you hear playing back after recording a track would be a little off in timing (lag) to what you are hearing that has been already recorded.
You can input a guitar on the right side input of the babyface and in TotalMixFx it is Analog 2 channel Input (top row).
Software playing back through the Babyface is the middle row (read the bottom of the row), and the Lower row (third row) is the Hardware levels playing back, the Top Row in TotalMixFx is the Input level you are having through the automatic gain inputs. If the signal is too low that will show although you can raise the monitoring level in TotalMixFx to hear it and by using the wrench icon graphic to open up any channel in TotalMixFx and adjusting further the gain, but again if the signal is not sufficient incoming in the first place, then TotalMixFx will not gain any input - it only monitors. Same way with all the Rows with the Input and Output.
So yes, I plug my synth into the Analog 1 & 2 inputs (but if I needed more gain I would have to add a pre-amp or something like a channel strip between the synthesizer and the Babyface Analog 1 & 2 or either or both Inputs. That in your DAW you can see also perhaps before you record the input on the Track of the DAW.
That's about it, and it is in the manual. It may take a few readings to understand it but persevere with it.
There will be no effects going in on the recording at any time with the Babyface, not until you have recorded a track, are playing it back and loopback with the effects (reverb or echo or both) and re-recorded the playback onto another track in your DAW.
You can go direct (with my synth I use left and right output) or you can use a DI box if needed for a guitar because Analog 1 & 2 are not for guitar, but for anything else. The guitar input on the right side is high-impedance and if needed again to boost the signal before getting to your DAW, that is where other equipment may be used but again when I record guitar I have a guitar effects module so I go into the Analog ! & 2 inputs still (because the output warrants that lower impedance type of input like a synth.) Also a mic can be used in the Analog 1 & 2 inputs but again if you have to turn up the gain to hear it (top row of TotalMixFx too much you may hear hiss and noise) because again the input has to be sufficient into the Babyface in the first place, with any musical instrument or microphone you are using.
Straight off though my MK4 Sennheiser Microphone only had to be turned up to a Gain (inside the wrench graphic with the circle - knob gain control) to +12dB to hear it the same. Whether that would be loud enough into your DAW that can only be decided when you listen to the recording and look at the levels coming out of your DAW on each individual track. (The Babyface monitors the output that the Babyface is putting out according to anything playing back through the computer - but again that depended on the input in the first place to begin with.)
There is 48phantom power on the Analog Inputs also in the Babyface if needed for a microphone, and also if you have the levels of the faders down in TotalMixFX then you will hear nothing. TotalMixFx yes, has to be used unless you control the levels on the Babyface its self (which can also be done.) Since I am working on a computer, it is just easier to use TotalMixFX and leave the Babyface dials and all of that stuff alone, but either or I guess.
There is no gain on your DAW input either when setting up the inputs and outputs. So in your DAW you see what the Input is also, but too high in volume or too low is all that you see. You can record wherever in volume, but then what it sounds like when playing will be how well you recorded the signal input in the first place.