ef flag is enabled, you will begin the seed with two characters and access to the Epoch, but the Epoch will not have its wings. Instead, there's a new Key Item hidden somewhere: The Wings of Time. When you find the Wings, bring them to the Snail Stop in Porre in 1000 AD. Dalton will be waiting there to receive them, and the Winged Epoch will be waiting outside. At this point, you can continue the seed as normal.
It is possible for the Wings of Time to be the Key Item at Snail Stop, which negates the flag almost immediately. While so far we have manually vetted seeds to make sure the item isn't there, in the future it will be prevented from ever showing up at Snail Stop.
Without the wings, the Epoch is accessible and usable, but it can't move around on the world map. Access to time periods is the same as usual; you will need the Gate Key to unlock Prehistory, the Pendant to unlock the Future, and either one of them to unlock the Dark Ages. The Epoch's location in each time period:
Remember that in most cases, the Epoch will remain exactly where you left it, but there do exist triggers that will move it automatically:
Locations inaccessible without the Wings of Time include: Sun Keep (all eras), Choras/Northern Ruins (both 600/1000), Giant's Claw, Ozzie's Fort, Sun Palace, Geno Dome, Death Peak, Black Omen (you can finish the game in Magus or Tyrano Go Mode without the Wings, but they are required for Black Omen).
Rarely used in standard flags, Gates and other walking routes are very important in this mode.