Hi DufauB,
Two boats for this crossing is completely normal. It’s not the subway, after all! :-)
The company doesn’t matter much—it’s mostly about the schedule and price that work for you. Some faster boats are twice as expensive.
You don’t need to book the boats in advance; June 5th is a weekday, and Greeks usually buy their tickets the day before or even the same morning via the phone app.
Booking a week or two ahead is more than enough.
Also consider the option of flying from Athens to Milos with Aegean or Skyexpress. Sometimes the flight ticket is as expensive as the boat! The flight takes 20 minutes, while the ferry takes about 4-5 hours.
To get to Piraeus, you have the metro. Either take line 1 (green) if, for example, the closest station is Thissio, or line 3 (blue) if you’re leaving from Syntagma.
If you’re leaving from Monastiraki, you can choose between both lines!
Personally, I find line 3 more comfortable.
Have a great trip!
Elenitsa