You can try that for the low level side- see if it works.
You're right, with a high level input- the signal is passing through two amps. Not ideal, but it's just a subwoofer and without an aftermarket headunit your options are limited to avoid the factory signal processing.
I'll start with the factory amp inputs first. If that doesn't work, it is "okay" than to route through the factory amp and then through the Eclipse? Others have done it that way??