Andrew,
        I consider myself somewhat of a novice at double side reflow
since I have been doing this for only about 5 months but here is my two
cents of advice.
Step 1: Determine which side you are going to reflow first and which
side is second.  As a general rule look at the weight of the component
to surface area of the pads ratio for each designator.  If you have over
30 grams per square inch for any component, odds are that component will
'fall off' the board if it is run first.  Therefore you know to run the
other side first.  That is great if no components on either side violate
this rule or if components on only one of the two sides violate this
rule.  What do you do if both sides of the board have components that
violate this rule.  Pick one side and use solder paste and surface mount
adhesive to keep the 'heavy' part on the board.
Step 2: Your reflow profile for side 1 is determined the same way you
create a profile for a normal job.  For the side 2 profile I do
something a little different that may or may not be correct.  I turn all
of the bottom heaters to 150 centigrade.  Most of the heaters will
maintain this set point with the exception of the 3 or so zones opposite
the reflow site.  These will typically equalize somewhere around 175-200
degrees centigrade so I set them at 5 degrees below their equalized
point.  This helps to minimize the heat to the bottom side but it
results in a greater variation in topside heat across the width of the
oven.  So far I have been able to live with this.
        Hope this isn't too far off base and that it helps.

Regards
Wade Oberle
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