Yah, I'm not absolutely sure because I'm no studio expert and/or I haven't dabbled in the recording end enough yet.. but if it's like my setup, seems when I have two of the inputs used on my Tascam interface, and the knob that controls the levels of the two is set in the middle, it seems to be lower strength than if it's set all the way to one or the other.
I've got Ableton on my DAW, and they recommend recording instruments in separate passes.. lay down the click track first, then record your bass, or guitar, or drums, then do a separate take for the next instrument. There are a couple of switches on my interface that I haven't quite explored yet that may affect the output.. one is of course, setting the input to guitar where the 1/4"/xlr comes in, and I'm sure you've got that set.. but evidently it changes the signal strength (I think it boosts the guitar and then if you're using that input for a mic you've got the option for phantom power). The other is there's a mono/stereo switch. I've always used mine in the stereo setting cuz I'll have my drums patched in by the midi input and my mp3 coming in on the 1/4" mic/guitar input so I want both stereo. But I vaguely recall reading in the instructions that if you switch to mono you'll get a better mix if you're then routing the two out at the same time to a pc or otherwise. I should test this.. I keep wanting to try recording and mixing and so on but never seem to get the time to learn all the great tech I'm collecting