Bookmarks are Outlines.

use PDF::API2;

$pdf = PDF::API2->open('PDB_TT_TimeVault.pdf');
$pdf->preferences( -outlines => 1 );
$page = $pdf->page(1);
$otls = $pdf->outlines;
$otl = $otls->outline;
$otl->title('foo');
$otl->dest($page);
$pdf->saveas('new.pdf');
[download]

makes a 2 page pdf into a 3 page pdf and foo is a bookmark to the new page 1. i'm not quite sure of the proper usage.