Best connection from Gaia to laptop is via USB cable (just USB A -> USB B). This will set up virtual MIDI ports through the cable, as well as an audio in- and output interface. Advantage of using this audio output is that it is digital, so this will give you the best audio quality when recording from the Gaia.
As for using your Gaia as audio input, indeed you can connect to the Gaia’s line-in input on the front panel and mix it with the Gaia’s output. Audio quality will probably be similar to your laptop’s line-in port.
Latency does exist but is pretty good iirc. Depends on what you want to do.
About plugging your guitar into your Gaia, I’m not super familiar with guitar signals. If it’s a regular line-in signal it seems OK, but I worry that perhaps the voltage may be too high or too low. If it’s too high it may damage the input port. If it’s too low you may need to use a pre-amp. Do you normally connect your guitar directly to your laptop’s line-in port? If you do then it’s probably safe.
I don’t have any suggestions for USB microphones

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