I have recorded an acoustic guitar into Cubase SX, both with a mic and DI'd. As I had expected, there are some phase issues. Having read a relevant SOS article, I zoomed in as much as possible on the two waveforms and tried to align them so that they are in phase. The problem is that the two waveforms are almost completely different! There is no way that I can align them. What can you do in such a case?
SOS Forum Post
Technical Editor Hugh Robjohns replies: The two waveforms will be very different, so trying to find some point with which to align them in the middle of a 'strum' will be difficult. Try lining up the beginning of a strum instead, or alternatively, take a look at the SOS review of the Little Labs IBP for another way to tackle this problem.
However, the very different tonal characteristics of these two sources, and the inherent timing variations between the microphone pickup and DI as the guitar swings back and forth slightly during the playing will mean that phasing is likely to persist as a problem unless the signals are a) panned apart (although listening in mono will bring the phasing problems back again) or b) one of the sources is kept very low in the mix.
Perhaps you should really be asking yourself why you want to mix these two sources together in the first place. What does one source lack that you think the other brings to the party, and could you achieve that desired sound by using a different mic, positioning it differently, or processing the DI signal in a different way?
I find it always pays to follow the KISS principle ('Keep It Simple, Stupid!'), and mixing two signals from the same source is always going to make life harder than it needs to be!