Note: The difference below is that there is one method for noting both single-syllable and multiple-syllable variant readings. You'll see that those discreet sections no longer exist.
Add curly braces { } around the syllable(s) in the base edition of the text and insert the footnote after the close curly brace. Example: the base edition reads བསྙན་དེ་ (bsnyan de) and the PRC reads བརྙན་འདི་ (brnyan di) on page 45, line 2. The body of the text looks like this:
and the footnote looks like this: