Yeah you can connect the amp with the speaker level inputs. That means that you connect your orignial speakers wires directly to the amp, and from their you connect additional wires from the amp to the speakers.
You can also buy a eq with a preout that mounts in the dash or in the trunk (better choice) - if you are powering sub(s) with your amp this is the way to go, since it will allow you to run all the speakers in your car instead of sacrificing any in order to satisfy the speaker level input configuration.