Yeah, that Scarlett doesn't have much headroom, so use the line input (the line level signal is much stronger from the instrument level signal), especially since you have EMG, so you won't have much signal degradation. Even with passive pickups it won't sound totally bad. I know that because sometimes I forget to switch to instrument input in my Saffire's MixControl software, and it doesn't sound that bad, it's usable for practice but you have to crank the input gain (I have Duncan Distortion). With EMG that difference is a lot smaller, 'cause they don't need that high HiZ input.