the head unit amp will always work.
when i have said connect behind the head unit you would basically be doing the same as connecting to the speaker wires in the boot. (there is no plug or wire in the head unit for this) the converter does not turn off the amp or fit in the head unit, its 'in line'.
the high/low converter is exactly for this reason, ie it receives amplified signals, it then converts these down to unamplified signals.
so whether this is done behind the stereo or just before the amp, its makes not too much difference. as long as you get low power to the amp.
ive eddited my last post as it wasnt clear on that.

you want the rear speaker wires to go out of head unit, and instead of going to the rear speakers they go to the high/low converter. the low out put (RCA) then goes to amp.
as for connecting the remote wire... well, there is two routes hear, one would be to connect the any wire in the boot that only works when ignition is on. this would mean amp is on when ignition is on rather than when stereo is on.
if you wanted it to operate when stereo is on/off then you need a stereo wire. the only ones in the boot would be the speaker wires. this would be a bit of a bodge, ive never tried it and i would imagine it could cause interferance. however it may not.
other wise connect it to the switch live in back of stereo.