The pre-outs will typically be the RCA style plugs, whereas those in the combination connector are usually to be wired directly to the speakers if using the head unit's integrated amp.
Edit: your head unit's instruction manual should clearly call out which are which, and if it's like my...
For those of you having audio issues while retaining the factory amp, you are using the pre-amp outs on your new head units, correct? I'm not sure why some are having issues and some aren't. Conceptually as far as I understand it, swapping this way keeps everything setup the same as from the...
My $0.02 having done option 1 on my 99 LX with Nakamichi.
There are two main avenues you can go down here:
1. Build harness adapter using Toyota connector or splice directly into factory wiring, retain Nakamichi amp, swap head unit. Very easy and straightforward.
2. Replace head unit and...