Yes, this is explained in-depth the help file under the Reference > Command Line Switches section.
If the site is named "site1" and exists within the root of the Site Manager then you'd use something like
FlashFXP.exe \site1
Or if the site is named "site1" and exists within a group named "group" in the Site Manager you'd use something like
FlashFXP.exe \group\site1
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