I'm curious if there is a proper way to format the furigana of words such as 足し算. Should the し be included in the furigana, or should the furigana of the each kanji be separate?

The furigana is just the reading of the kanji, the し is just a し, so it doesnt belong to neither the 足 nor 算. One good way to test furigana readings is in the word 2007 using the fonetic guide there (I think you need to have japanese language installed as well).

Thanks, that is what I was thinking. It is a bit confusing though, because the automatic reading generations in Anki include kana as well.

Is it using "Tashi" over 足? Or "Ashi"?
Ashi is one of the readings, but not the right one when together with "-し算". The right reading should be Tashizan, with only the "TA" as furigana over 足. (sorry, but Im on a laptop that cant type Hiragana )

Yes, you are right. The reading is たしざん meaning "addition." Thanks for your insight about the furigana.