I'd recommend taking the signal from any pickup if fitted, plus the signals from two mics - I prefer one at 90 degrees to the neck, about as close as you can without clouting it, aimed at the neck/body join and another at about 45 degrees pointing at the soundhole from the tail direction.

It's important to keep the signals separate and try to get the best possible clean and natural sound. You can blend them, change EQ and add reverb/echo/delay/chorus to taste at a later stage.

Remember, you cannot take effects OFF a recorded signal.