John, the below listed information comes from Sonic Electronix.
I hope this helps.
High-Level (Speaker Level) Inputs:
Speaker level inputs are commonly referred to as high-level inputs and vice versa. Some amplifiers will have special adapters with bare wire at the end, this wire will connect to your speaker wires. Speaker level inputs are used when you want to connect an amplifier to your factory radio or an aftermarket radio that does not have low-level (RCA) inputs. It allows you to use the signal coming from the speaker outputs as an input source for the amplifier.
Low-Level (Line Level) Inputs:
Line level inputs, also known as RCA inputs or low-level inputs, use RCA interconnect cables to link the amplifier with the source unit. Most aftermarket radios have multiple pairs of RCA outputs that can connect to multiple amplifiers. Factory radios, even those with stock amplifiers, often do not have low-level inputs so these are used mostly with aftermarket setups.
Is there a difference in sound quality between the two input methods? Factory stereo systems connected with high-level inputs will not sound as good as low-level inputs. If your using an aftermarket stereo, there wonít be much of a difference between high-level or low-level inputs on basic systems. If youíre going higher end use low-level inputs. Often times high-level inputs are connected incorrectly and as a result there is signal degradation. Because high-level inputs require that you splice into your vehicle wiring, some users forgo that option and prefer to run the RCA cables instead. These input methods give great flexibility when installing into vehicles regardless of their system type.
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