How To Run 2 amps with one RCA?

Run the full range RCA's into the 4-channel amp.  The amp has crossover settings for the fronts and rears, so set both to high pass and set the low limit to about 80 Hz.  That amp also has a full range output to connect RCA's to the sub amp.  Set the sub amp on low pass and also at about a 80 Hz high limit.

The crossovers on the components will split that 80 HZ and up signal to the mid and tweeter.  If you want the fronts or rears to play lower than that you can use the adjustment on the amp, but you generally don't want to play the sub freqs on the mids as it will distort the rest of the sound.  The rear coaxials can be attenuated by adjusting the amp gain to a less sensitive setting. 

 I don't see a need here to add an additional crossover to the system.

Your JL350/4 or 450/4 should have a pre-amp output to "Bi-Amp" your second Amp (1000/1).  Use a Heavy Gauge Sheilded "Y" connector to run all 4 channels and then run a second set of RCA's from your 350/4 or 450/4 pre-amp out puts into the 1000/1 input terminals. Set your 1000/1 for low pass and you should be running both amps from 1 set of RCA's from your deck.

If all else fails, read your owners manual, page 9, tells you how to bi-amp in 3:1 or 5:1, modify as needed