I have a JVC KD-SX980 in-dash MP3/CD/tuner with 2 pre-outs; one front;
one rear. I just received my amp and subs from UPS today. I had
planned on using the head unit to run the 4 speakers in the car and
use one of the pre-outs to run my sub amp.

I was perusing the install paper for the JVC head unit, and it says to
disconnect the speakers when using an external amp and tape off the
wires (in bold letters). The install paper mentions a different model
head unit with a subwoofer output. There are nifty diagrams for
wiring dual amps for front and rear speakers, but no mention of
running a sub with this particular head unit. I presume the text is
there (in bold) so folks will know to disconnect the speakers from the
head unit if one is using external amps for front or rear speakers,
and to tape off the unused speaker leads from the head unit so they
don't short out.

I should be able to run the 4 in-car speakers off the head unit and
use one of the pre-outs to run my in-trunk amp and subs, yes?

The instructions have me confused. I won't damage something?

you will be fine running the speakers off of the head unit, and the subs off
the RCA output. you only disconnect the speaker wires and cap them off if you
are going to connect them to their own amp. what they mean by that is that when
you install an amp, those speaker wires are disconnected and the speakers get
their input through the RCA