$证明:(1)∵四边形ABCD是平行四边形,\ ∴AD=BC,AD//BC,$
$∴∠ABC+∠BAD=180°,$
$∵AF//BE,∴∠EBA+∠BAF=180°, ∴∠CBE=∠DAF,$
$同理得∠BCE=∠ADF,$
$在△BCE和△ADF中,\begin{cases}{∠CBE=∠DAF,}\\{BC=AD,}\\{∠BCE=∠ADF,}\end{cases}$
$∴△BCE≌△ADF(\mathrm{ASA}).$
$(2)解:∵点E在▱ABCD的内部,$
$∴S_{△BEC}+S_{△AED}=\frac{1}{2}S_{▱ABCD},$
$由(1)知△BCE≌△ADF,∴S_{△BCE}=S_{△ADF},$
$∴S_{四边形AEDF}=S_{△ADF}+S_{△AED}=S_{△BEC}+S_{△AED}=\frac{1}{2}S_{▱ABCD},$
$∵▱ABCD的面积为6,∴四边形AEDF的面积为3.$