Traveling between EU countries

In simplest terms, you go through the line based on the passport you hold, not where you've been.

The pattern will make comeplete sense when you return to the United States and look at those lines.

The UK isn't part of the Schengen treaty, so when you arrive at Athens, you (and all other passengers on your flight) will have to go through Immigration (passport control), and Customs before exiting the airport.

While England is a member of the EU, it is not a party to the Schengen treaty, so I think you will have to go through immigration because you don't have an EU passport. Generally, you can move freely within Schengen countries -- such as from France to Germany -- without the need to show your passport. But, when you go from the UK to, say France, you have to show your passport because the UK is not part of the Schengen zone.

Immigration is separate from customs.

For immigration (aka passport control), the lane you choose is based on the passport that you hold. Thus, you will go through the non-EU lane.

The EU has a customs union so for customs, EU contries typically have three lanes:

Blue - travelers arriving from EU countries

Green - nothing to declare

Red - goods to declare

If your journey originated in an EU country you may go through the blue lane. However, there is no problem if you go the green lane.

You can use the blue lane, since you have been through customs in London and have been in London for more than 24 hours, and are thus not arriving directly from the US.