yes, selective transfer is the feature you are looking for
from the gui, to use it, you would create a selective list, choose it, then schedule your transfer. to transfer automatically using the selective transfer feature, we'd need a command line switch for it. I will see about adding this feature before we release final, as it indeed, could be extremely useful.
Example:
using windows scheduler, setup something like this:
flashfxp.exe -c2 website.fqf -s="Name of Selective Transfer ruleset"
this would start flashfxp, load and transfer the queue file website.fqf, using the specified ruleset, and close flashfxp when done.