I had the steam version but once I saw it here on gog I had to get it.

However I am trying to figure out how to unlock second wave options.

All of the articles so far refer to steam...is there a way to turn them on in the gog version (I thought with all the updates it would be enabled automatically or a root menu option.) but I have not seen it.

Thanks!

In Enemy Within, some are selectable right from the start. New Game -> Second Wave

In Vanilla XCOM, they only show up after you beat the game, and the unlocks depend on the difficulty level you completed the game on.

Not entirely sure, but I assume further second wave options are unlocked when you beat Enemy Within. It's been a few years.

Found it, before I was using a mod where they were in the main menu. For the gog version they are on the left bottom once you select a new game.

Now to figure out how to apply mods...everything I have has been tailored to a steam install...

It's exactly the same.