In my opinion and experience, you are better off using a line level input. A speaker level signal will have a little more distortion and it will be converted back to a line level signal by the subs speaker level circuitry anyway, but it will still contain the distortion created by your main amps output.
If you noticed more detail in the bass notes after disconnecting your current subs it maybe because you have the low pass filter on the subs set too high, enabling too much frequency overlap between your subs and your F208’s. The 3 db down point on the F208’s is 31 Hz, so you might be able to set the low pass filter slightly above that, but more than likely it will have to be set below that, which unfortunately doesn’t leave much for your subs to do. You may want to consider high passing your mains which would lessen their work load and also reduce unwanted cabinet vibrations created by F208’s low end drivers giving you even cleaner and more detailed sound from your mains.