I have the A1SR (the version after the one you have), and you can either, as Jase says set everything in the Toshiba, or, at least on the A1SR, change the EXT-1 settings to DSP, which converts the analogue signal to a digital signal where it then undergoes DSP processing hence applying all the settings (speaker config, level, delay etc) that are applied to all other settings. There is a further, irrespective of whether you select analogue or DSP, setting for the subwoofer, where the default is +15 dB, which is what i have stuck with - anything less and there was a noticeable lack of bass.
I have everything set on the Toshiba to LARGE, with no distance or level adjustment. I also select "Don't Use" on the subwoofer to avoid applying 2 cross over adjustments - once in the toshiba and again in the amp. Following earlier advice, i have also selected SPDIF to PCM, and DRC and DE to OFF. Crossover is set at 120 Hz, but i am assuming it has no effect if the sub is set to off(?) There is certainly no shortage of bass when i play dvds, whether SD or HD-DVD, through the analogue outputs of the toshiba, and the sound is fantastic - as comparable and tight as from my Denon A1 dvd player over Denon Link.
As an unrelated point, and I've seen other posts on this, I have to say i can't tell the difference between DD+ and True HD. Irrespective of the settings I've mentioned above, I have pretty much tried every combo including applying all the base management settings in the player and setting the amp to analogue for straight pass, althrough I still cannot tell the difference when i switch between the 2. For reference, i have version 1.3 software, which i have never updated since i got the player. This last part is the only niggle in an otherwise near perfect set-up.
Certainly welcome any comments on the above