You are correct.  The lower "bleeder" is to remove old fluid from the
lower cylinder.  The upper bleeder is to remove the air (air rises!)

You can open the lower bleeder and press the pedal repeatedly until
new fluid comes out.(just keep checking the master cylinder fluid
level).  Then bleed the upper valve like one piston calipers.

If your caliper seals are grungy, you may want to remove them and
clean/rebuilt the calipers and pistons etc.  Not too difficult, but
messy and time consuming.  Rebuild kits should be under $20 per
caliper (two outer seals and two inner seals needed per caliper)

this Porshe link below will help explain the rebuilding procedure
(the 84 and older Vanagon dual piston ATE calipers are very similar
to the 911 calipers in this article)....and whatever you do, DON'T
separate the two halves of the caliper.  They may never work properly
again if you separate them.
http://www.pelicanparts.com/techarticles/911_caliper_rebuild/911_caliper_rebuild.htm

This is an especially good tip from that site, applicable to all vehicles:
>      Depress the brake pedal slightly, just to the point where the
>brakes would be beginning to engage, and block the pedal in this
>position. This will prevent all of the brake fluid from draining
>out, and a lot of air getting into the brake system, when you
>disconnect the caliper lines. I use a piece of wood with a notch in
>one end and a small square of plywood to protect the seat at the
>other. With this setup, you can move the driver's seat into position
>to keep pressure on the brake pedal. (Figure 7)

>I did try flushing using just the upper valve, but then when I cracked
>the lower to see what it did, noticed that I got some old fluid from
>there.