You might want to try using the RCA outs for your upper range signal and the LCR outs for your bass. There's a little difference in the gain, but I see no difference in the quality.
That will create a roughly 3dB difference in gain for the low frequencies vs. the high frequencies. That's enough to throw things off quite a bit. Better to split one output so you have the same signal gain going both ways.
When you bi-amp, aren't you eliminating the speaker's internal crossover?
Not the way we're talking about it. This is passive bi-amping, which only serves to increase the power available to the speaker. In most cases, the benefits are negligible at best, but with an especially difficult speaker to drive (like the Polk LSi's) it may be more useful.
The only way to remove the internal crossover from the mix is to do active bi-amping, which requires building a crossover network to include between the pre-amp and the amps. That crossover network then handles splitting the signal and sending it to two or more amplifiers. After that, you have to physically remove the crossover network from the speaker and wire straight from binding posts to drivers. This is a very complex process and requires both technical expertise and knowledge of the speaker's design.