Yes, you could do that for the high level inputs (with the JL amp). Some other amps accept high level (speaker wire) inputs but generally they don't sound as good as a line output converter. Consider the distance to where your amp will be too, if you're going to mount the amp in the hatch somewhere you would get a cleaner signal with less chance of noise by running a line output converter and low level RCA's to your amp. You can get a cheap non-powered PAC adapter for something like 15 dollars, or get a powered one like the audiocontrol and get a cleaner signal and run a higher voltage to your amp.
Kipperman, that is the amp I almost got but I found the Polk PA D5000.5 on amazon that is almost identical except it has a more powerful subwoofer channel and comes with the remote gain module for $290 and free shipping. You can also run a single pair of RCA cables to it and it will automatically send the signal to all the other channels which is a nice feature if you need it. I will be installing mine Friday and can give more notes on it then.