You don't have to rely on JRunner for something as simple as that.
I've not used the JRunner application yet, so I cannot speak on its behalf, but that would be a no brainer to me.
I would assume you select your "freeboot" image the same way you select your stock image.
Write your "freeboot" but select your stock nand the same way you do in jtag tool and let it write it for you.