This article shows how to change the position of the thumbnails.

You need a Professional or a Premium license to do this, because you have to edit source code.

(follow this article to dowload source code : http://www.radaeepdf.com/support/knowledge-base?view=kb&tmpl=component&kbartid=2) 

You have to edit thumbOpen method of PDFThumbView class as following:

public void thumbOpen( Document doc, PDFThumbListener listener )
{
   //m_thumb.vSetOrientation(2);//RTOL horizontal layout
   m_thumb.vSetOrientation(1);//Vertical
   m_thumb.vOpen(doc, 8, 0x40CCCCCC, this);
   m_thumb.vSetThumbListener(listener);
   m_thumb.vResize(getWidth(), getHeight());
}

You have to edit the last lines of reader.xml as following:

<com.radaee.util.PDFThumbView
    android:id="@+id/thumbs"
    android:layout_width="50dp"
    android:layout_height="match_parent"
    android:layout_above="@+id/bar_find" />

If you want the thumbnails on the right side you have to edit reader.xml as following:

<com.radaee.util.PDFThumbView
    android:id="@+id/thumbs"
    android:layout_width="50dp"
    android:layout_height="match_parent"
    android:layout_above="@+id/bar_find"
    android:layout_alignParentRight="true" />