is the OP talking about automation or audiosuite? i'm so confused by this thread!
i know he mentioned pencil tool, so i guess it's about automation, but if it's audiosuiting something that's another case entirely.
if it's about audiosuite, then there IS a way to apply EQ to all subclips. just set the plugin to OVERWRITE and it will apply to all subclips. i've done this many times where i've edited a buttload of audio, only to find out the mixer wants to add some dc removal or HPF. i can do this without upsetting my timeline or having to zoom in to every region in a multi-hundred minute project.