There's notarization service available in the Tainan City courthouse. I think it's only available in the morning. They can notarize documents in English and it was accepted by the government in the US. Very friendly and quick.

Also there is the info you need to get your marriage registered by the court.

308, Sec. 3 Jian Kang Road.
06-295-6566

聯絡地址：70802臺南市健康路三段三○八號
聯絡電話：(06)295-6566

District Court page: http://60.249.218.170/index1.asp

marriage info at: http://60.249.218.170/P04_01.asp