Littlefinger was named Lord of Harrenhal and Lord Paramount of the Trident. The Freys got Riverrun. Are the Freys therefore bannermen to Littlefinger, or do they now have a "great house" status owing direct allegience only to the King. Ran and I have been trying to figure this one out and are stuck.
Technically speaking, the Freys are now bannermen of Petyr's yes... assuming that Tommen and Joffrey are regarded as legitimate kings, entitled to make such dispositions.
In practice, it remains to be seen how deferential the Freys will be.
Take care, and good luck writing A Dance with Dragons.
I'll need it...