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I have an HSE and it has the 6CD-645 head unit that is tied to the fibre optic NAV and underseat amp.
I regard replacing that unit with anything else suggests a new Nav display and underseat amp and who knows what else - in other words, a major project.
Am I correct of did the unit you purchased have the fibre optic hookups?
Mine is an SE so only had the CD400 without fibre optic system, there is a fibre optic harness but unsure what functions you will lose but from what i have read you will lose sat nav,cruise control and clock - i only lost the clock.
The head unit GPS is probably better and possibly could output to the factory screen as well.