No you will not be sacrificing any sq by doing it this way. You will actually gain some since you have more control over the crossover points and the eq of the system. Take your time and tune it. As for the 6600 for what it does I love it. I use the nav and sat radio and the dual zone for video. For my competetions it is not the best HU for that. I do not like the fact it does not have T/A or crossovers, and it is a powered deck. i wish it was dead. But since I drive my car every day and I have to entertain a 8 and 3 year old it works out great.