It shouldn't have any effect on the sound quality. Technically the source is only two channels (CD, Radio, MP3), even if the head unit has 6 or 8 channels of output it is just splitting the original two-channel (stereo) source. In your case, the Clarion EQ only has a 2 channel input so everything after that is split anyway. The fader on your EQ wont do anything, but you will be able to control the subwoofer level from the EQ. The only way it would cause a problem is if your head unit had time alignment, but it doesn't look like you have a head unit with T/A, so you should be all set.