Owlboy's map is a set of floating landmasses grouped into named regions. Progress is not a simple left-to-right line - the Anti-Hex scattered the islands, so the map is a web you reopen from multiple directions.
The floating owl village, and the game's home base. Vellie is where Otus lives before the owl cloak, and where the game returns you between regions. The sky pirate attack on Vellie is the event that starts the story proper, and the destruction of the capital city Advent is what gives the campaign its weight.
The lower and middle altitudes of the sky world, and the first regions you push into once you have wings. These are the areas that teach the cloud-and-vent interaction, the throwable companion, and the trick of using sludge rather than avoiding it. Mesosphere in particular has the vertical structure that makes gliding feel like a power rather than a slow fall.
The large central landmass and the main hub of the mid-game. Most of the game's remaining owl relics and the bulk of the platforming vocabulary live here and in its connected regions. It is also the point at which the game stops being a gentle introduction and starts being a real metroidvania.
The high, late-game regions. The Eternal Sanctuary is the series' version of a sacred, dangerous place, and the Owl Temple is where the relic mythology and Solus' plan come to a head. The Temple's role is also mechanical: it is where the game's trickiest platforming and its hardest optional fights are concentrated.
There is no fast travel in the original game, so route planning is a skill. The practical method is to pick two or three things you are hunting on each pass - a relic piece, a companion, a token - and to sweep the region you are already in rather than bouncing across the map. The 10th anniversary update's Super Dash closes some of the smallest gaps, which makes backtracking noticeably less painful than it was for the first eight years.