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