I've tried it both ways, and makes no difference in the sound. I have both 1290/2's and 1590/2's, and have used the PA-1's on both. To me, the sound from those amps is too lean in the midrange, and I sold them. A better way to biamp is with the ADS C2000 x-over and two identical stereo amps, but that can get expensive. Also, the C-2000 must be modified internally, which is quite easy to do, to make it work with those speakers, as it was originally designed to work with the L1230, L1530, L2030. All biamping ever did for me was to increase bass output, which can also be accomplished by adding a subwoofer. I currently use the above mentioned speakers with a McIntosh MC7200 amp + a Velodyne F1500R sub, running the speakers full range and adding in the sub output as needed. This has worked out great for me.
To answer your ? simply, I didn't find any difference in how you connect it. The distance from your preamp to speakers, and distance between speakers may dictate which method you prefer. Happy listening, the 1290 is a superb speaker, even by today's standards!!!