In that configuration, I would use hte rear outputs and connect your line level converters to that.
I believe that this will exclude things like warning chimes from being run through your amplifier, which is a good thing. It will also provide some level control via the fader.
For summing the tweeter and woofer channels, I would avoid this if at all possible. There exists some possibility for undesired feedback, even if it does not damage the amplifier output devices. Without spending some time studying a schematic for the head unit (Which is never going to be provided) I believe that the risk is unacceptable, given the cost of replacing. Almost all 12V amplifiers are designed to run in BTL mode, as opposed to a common ground. Good aftermarket "bridgeable" amplifiers usually run common ground, but this is almost never the case when the amplifier is integrated into the head unit, even in the best aftermarket units, and so far as I know, never in factory units. This makes any kind of summing of the speaker outputs risky.
I did not know that there was a 9 speaker version of the Sony sound system, nor that it was available with Sync1. I have the 10 speaker (North American) version with the sub and amplifier, and MFT setup.
There is one configuration that might be possible, and safe to sum the signals, and that is to use line-level converters on all 4 channels separately, then sum the high and low signals afterwards with a Y cable. Pre-amp signals are much easier to sum that way, and far less sensitive to feedback, since the output devices aren't dealing with much real power, and are generally very high impedance. This costs a little more, but think of it as insurance.
In this case, however, I believe that it might also be worthwhile to consider an additional, smaller amplifier for the tweeter signal. Run the mids and subwoofer from your 3 channel amplifier, and run the tweeters from a smaller 2 channel amplifier. Other people go to great lengths to get that bi-amped setup.
2012 Focus Titanium Hatchback
121,000 km, all stock
1990 Toyota Supra turbo
I think the cams are still stock...