(Some of the details below may vary by device. I'm speaking of the Gospel Library for Android.)
If you read with the footnote pane open and beside the scriptures, it's pretty easy to notice JST entries (the ones where the text is in the footnote are black text rather than blue links, thus making them stand out). I've found that it was easy to get into the habit of viewing in landscape mode with the footnote pane to the right and noting any time the JST came up in the footnote.
Also, you can highlight the JST footnote words (you can't highlight just the letter - at least, I couldn't) - but just like your paper scriptures, you have to manually mark each one. If you're going to do this, I recommend you choose a color and whether to use underline or highlight, and then use that color and style consistently, since you're looking for a quick and easy alert that there's JST text to review...
FWIW,
Liz