Should I add my index after the table is populated or before (MySQL. Aurora)
Have the primary key in place, but not the secondary keys.  When finished loading, add all the secondary keys in a single ALTER statement.

Caveats:


I have not done that particular task, so I dont speak from experience.
There have been changes over the years in how ALTER works.  Doing multiple alters at once used to be optimal.  But with online/instant/etc ALTERs, it is hard to say.  Still, the current ALTER .. ADD INDEX.., even though it comes back instantly, has a lot of work to do afterwards.
If the PRIMARY KEY in not in place to start with, it will have to reorganize the data.  However, this aspect may depend on whether the source data is in PK-order.