Should tone sandhi be written in pinyin?
Tone Sandi rule should merely apply to spoken. In written, you should always put original tones in any forms of exams except that those exams are testing the rule itself. 

In fact, I doubt most of natives are aware of the existence of Tone Sandi indeed. But they do apply the rule naturally in practice. I suggest you study by phrase, not by character. That way you will know how each character will be used and the way to pronounce in practice.