(1)解:$\because$点$A(1,6)$是反比例函数$y=\frac{k}{x}(x>0)$图像上的一个点,$\therefore k = 1\times6 = 6。$
$\therefore$此反比例函数的表达式为$y=\frac{6}{x}。$
(2)证明:$\because$点$A,$$B$在双曲线$y=\frac{6}{x}$上,$AD\perp x$轴,$AC\perp y$轴,$BF\perp x$轴,$BE\perp y$轴,
$\therefore S_{矩形ADOC}=S_{矩形BFOE}=6。$
$\therefore S_{矩形ADOC}-S_{矩形ODGE}=S_{矩形BFOE}-S_{矩形ODGE},$
$\therefore S_{矩形ACEG}=S_{矩形BGDF},$
即在点$B$运动过程中,四边形$ACEG$的面积与四边形$BGDF$的面积相等。
(3)解:$\because A(1,6),$$B(m,\frac{6}{m}),$$G(1,\frac{6}{m}),$
$\therefore AG = 6-\frac{6}{m},$$BG = m - 1。$
$\because\triangle AGB$的面积等于四边形$ODGE$的面积的一半,
$\therefore\frac{1}{2}AG\cdot BG=\frac{1}{2}EG\cdot DG,$
即$(6 - \frac{6}{m})(m - 1)=1\times\frac{6}{m},$解得$m = 2。$
经检验,$m = 2$是原方程的解。
$\therefore$点$B$的坐标为$(2,3)。$