you can use setRect method of PDFAnnot class.
e.g.
//get annotation instance at point
m_annot = [page annotAtPoint:m_annot_pos.x: m_annot_pos.y];
//create new rect
PDF_RECT rect;
rect.left = 100;
rect.right = 300;
rect.top = 100;
rect.bottom = 300;
//set rect of the annotation
[m_annot setRect:&rect];
// Re-render the current page
[m_view vRenderSync:m_cur_page];
[self refresh];
// Save the PDF file
[m_doc save];