I like Gwern’s treatment of footnotes: on a large enough screen, the main text goes in the middle, and the footnotes go at the sides, so you can flick your eyes to them while you’re reading.

If you can’t have that, linking to the footnotes and back to the main text also works well. Another quite popular option is to have a tooltip with either a summary or the main contents of the footnote: this can be good for quick links or due diligence reporting, but for long pieces of text I find it harder to read, and dealing with sub-footnotes without accidentally closing the whole thing can be tricky.