Her Majesty is a hidden track on the Beatles album Abbey Road, I assume you're talking about 'Endless, Nameless'? Typically (and from your description) this song is part of track 12 separated by silence from 'Something in the Way'. Why do you say it ripped it incorrectly, did it not verify against AccurateRip?
If you want to split this track into multiple parts it's best to do it after the ripping process (otherwise you'll potentially destroy all the other tracks). dBpoweramp does have some
DSPs to remove silence, but I don't think it'll generate an additional track for you, so if you really want to do this it might be worth doing it in an audio editor, as long as you understand you'll no longer have a bit-perfect copy of the CD.
If I was to do this (I've done something similar on other CDs) I'd split track 12 into 3 parts, reference all of those in the CUE sheet (under track 12) so I can still validate the rip, and then tag them as you like. I'd then hide the silent file from my player software using a custom extension and exclude it from scanning e.g. *.silent.flac
I believe one of the recent
anniversary editions does have this song split out, so if that's what you're talking about then ignore everything above :-)