But where in the chain is the best spot to add the x-over.
I'm sorry, but I don't understand the question.
If you're running the main speakers full range, then the only "crossover" is the low pass filter built into the sub.
If you want to remove the bass from the main speakers, then I assume a line level high pass filter would be inserted before the power amp. Thus, the bass is removed from the amp as well. You would still use the low pass filter in the sub. Or if you employed a bass management controller that provides both the high pass and low pass filters, you would want to by pass the low pass filter in the sub.