My brother in law came back after finishing university in the US and then returned to do his service. He applied for substitute service at the military office that was later approved. He subsequently underwent basic training at 成功嶺 for one month and then drew lots to be assigned to his duties.
To be eligible for substitute service, you usually have to have a medical condition, verified by a hospital, that makes you exempt from regular service. However, I’ve seen the rules expanded to accommodate overseas Taiwanese.
I suggest you report to your military conscript office （兵役課）at your local government office （區公所）when you re-register your household registry, and apply for substitute service before they send you your draft letter. Once that letter is sent, you will not have the opportunity to appeal. The local office and military office will provide you with the relevant info on what you need to apply for substitute service.
Usually, for English-speaking overseas Taiwanese, you will be assigned to teaching English in deprived areas. My brother in law was stationed in a small school up in the mountains in Xinzhu serving an aboriginal community. His duties were to design courses, teach, and some administrative work. At his post, there were 2 other substitute servicemen. He was required to live on the school premises during the week, but was free to go home during the weekends (if there was no school activities).
According to him, the work can be very rewarding- he was helping some of the most deprived kids in Taiwan. The work can also be very exploitative and tedious- thanks to a new lazy bureaucratic headteacher who treated them nothing more than slave labour.
Because of job requirements, you will most certainly be under pressure to learn Chinese very quickly. All administrative reports and documents are in Chinese. You will have to be able to read and write- or befriend someone to help you with that. 
That said, substitute servicemen enjoy far more freedoms than regular servicemen. By its very nature, you are serving in a civil environment rather than a military environment. Thus, there are fewer restrictions on what you will be allowed to do- i.e. my brother in law drove his car to and from the mountains, as a soldier you would have difficulty having this privilege; he shared an air-conditioned room with 2 other guys instead of 20-50 other guys; he had the freedom to use his own laptop and other electronic devices; etc., etc. (you get the idea).
At the end of the day, you will have had a crash course in Chinese and in patronizing Taiwanese bureaucracy culture. You will also have made some good friends or connections, which will become useful to you as a primer to life in Taiwanese society.
I wish you all the best! 
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