Okay, having done an experiment on this, I think I can easily say that it would cost less to book the two rooms together rather than seperately. YMMV though.

I chose a random town that has a 7% state hotel tax and no local hotel tax.

When I put in a $30 bid, one room, one night, the taxes and fees came up as $9.56 (the state tax would be $2.10, so the PL fee is $7.46) for a total of $39.56. Multiply by 2 for two rooms booked seperately, you get a total $79.12 (total PL fee is $7.46 x 2 = $14.92)

Now, I put in a bid for $30, TWO rooms, one night (so a $60 subtotal), the taxes and fees come up as $12.42 (state tax would be $4.10, so PL fee is $8.32). Total cost is $72.42.

Bottom line in this example, you'd have to bid at least 9 dollars less for the second room in order to about break even and/or save money by doing them seperately. And bidding the rooms seperately could put the second room in a different hotel. I think the only case in which this would make any sense to attempt would be in a small (i.e. one zone only) area.