Open site 1 (I call it left now) and site 2 (I call it right) in flash.
Choose the correct passive transfer mode.
Say we want to transfer a dir from left to right. Select the dir on right where you want the dir left placed in.
Select the left dir you want to copy and add it to the queue..
Log off from left and right.
Choose Tools->Schedule and fill in your options and then click on enable
Simple enough I would say...
Basically anything you have in the transfer window (left bottom window) will enter in the queue..
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