Let's start with Zera, as many of the characters would. It includes Cydonia and of course Quadragulia. Nephilim Tower is on an isle north of Quadragulia. Acidra is close enough to Zera to fight a war in. Lortia is within coach distance of Quadragulia, and is on the Lariel Ocean. Uiraray is 2 days west of Lortia, so Lortia probably isn't on the west coast.
Sata Andagee is far away from Nephilim Tower, so it might not even be on the same continent as Zera! We don't know much else about its location. Mt. Slaedro is two days away, and Titan's Spleen is within three days. Shirande's Northern Keep is near Titan's Spleen, which suggests Shirande and Santaj are southish. If Sata Andagee is temperate, this suggests it's in the northern hemisphere (if this is even a planet).
We don't know where Atrane is - maybe near Sata Andagee. To its south are Basilisk, Radon, orcs, and an ocean. To its north is Duradormir. Emmaghe is "eastern" but not necessarily close. Unfortunately none of these places are mentioned anywhere else.
Lariel Ocean seems to be in the middle of things, which is annoying since it's so hazardous to cross. Maple's first ship in Lariel when it was destroyed, and she washed up on Shiori Beach. The second time, after the Krakenhead attack, she wound up on the same beach again. So the Krakenhead is in Lariel, and the prevailing winds are toward Haato. The Krakenhead is also in Lortian waters, so the Lariel Ocean is adjacent to both Haato and whatever continent Lortia is on. Since Lortia has the Anoeith ships, it's probably close to the Altass Ocean too.
Haato Continent contains Shiori Beach, the Temple of Mirrors, and Seaside Town Hamasho. It's (sub)tropical, because it has palm trees. Inverse Babel (where So Damn Evil was found) and Durend (where Araceli was captured) are within a few weeks' sailing, so they might also be on Haato.
We know the continent of Yahnisil is across the Altass Ocean. Vinecliff is on the coast, and not the east coast, because the Forbidden Region is east of it. That it's on the way to the Forbidden Region suggests Yahnisil is eastish of Zera.
And then there's the sealed lost northern continent, but we don't know what's there.
There are a lot of places for which I haven't noticed any location clues:
- Eikard (whence Aileen)
- Saint Leon (whence Fatima)
- Durac Colony (whence Fluffy)
- Warplaiait, or however it's spelled (whence Path)
- Gigas' Gallbladder
- If Zeanogia is a place as well as a tradition of dark ETHER, it's near Gigas' Gallbladder.
- Guarandoo (of the ship Defagitable) might be a place.
- Zaagor Pyramid might not even be in the same world.
But we can guess that Lariel is between Haato and Zera-land, with Haato on the equatorial (south?) side. Altass and Yanihsil are most likely eastish. Sata Andagee's continent probably spans the north temperate-subtropical latitudes.
How much of this is right?