The X Rebirth game is set within a fractal-like network of Zones, Sectors and , [solar] Systems that are all within, so far, one Galaxy. There are multiple Zones within each Sector, and there are multiple Sectors within each System. There are different means of travel for different types of location, which are described below. There's a great-looking map here.
...
S/M ships, including the Skunk, may use regular (yellow or green) highways to travel at a faster speed between the zones within a sector. These features look like long, mist-filled , cylinders tubes where the flow of the mist indicates the direction a of travel. Different highways may have different rates of acceleration velocity to each other and along sections of highway, ; acceleration rates may vary too. Using boost in a highway increases the Skunk's acceleration ratevelocity.
In order to use a highway, we only need to fly into them and after which, the Skunk moves to the centre lane and begins to accelerate. We can control our speed and position within the highway at all times and the Skunk will stay within a given lane regardless of the shape of the highway if left alone. The easiest way to maneuver within a highway as a keyboard user is to press the space key to activate the cursor and then to use the arrow keys strafe to change 'lanes' if wanting to dodge slower NPCs (crashing into them will force their exit & slow you down). In order to exit a highway at any time, press the backspace key (not sure about joysticks/pads). Repeatedly crashing against the sides will slow you down and probably eject you, whilst shooting other ships can force them to exit. <Note - the outside of the highway lanes tend to be the fastest due to less traffic, but it's fairly easy to exit by accident - Snafu>
Regular highways are similar to Super highways, which allow S/M ships to travel between sectors (see below). Both regular and super highways are unidirectional, although they're often located near entrances to routes going in the opposite direction. Some sectors have relatively direct highway routes between their zones whilst others can meander around a bit. Either way, apart from within Radiant Heaven sector and the Teladi Outpost DLC sectors, the highway network typically offers the quickest route between zones for S/M ships. Sometimes on a map you'll see a couple of highways crossing each other. In order to change highways, simply exit one and enter the other.
Super highways between sectors
Blue Super highways are pretty similar to regular highways. Only S/M ships can use them and they are tubes that connect different locations ( sectors rather than the zones )within a sector. The Their main differences are that they cannot be voluntarily exited before reaching their end, and there are occasional fiery obstacles that slow the Skunk and/or drain shields unless dodged (stay in an outside lane).
Jumping between sectors by capital ships
...
This can only be achieved via Jump Gates, which require approach and flying through via free-flight (see above). So far, each system has at least 2 gates but some are inactive. Of the inactive ones, some are not in use by the game [yet] and some connect to the Teladi Fields of Opportunity system ("The Teladi Outpost" downloadable content (DLC)) - a trend that may continue with recent the announcement of a new DLC that is anticipated to arrive with or around the upcoming release of 4.00. Once a gate has been traversed, the ship will find itself within a new zone and from there, may continue on its way via the methods described above.
Note: if given a mission direction to travel to a certain zone within a sector, the easiest way to do so is boost to the highway then engage autopilot. The autopilot will automatically exit at your destination, whether it's at the end of a highway or somewhere in the middle
Additional info
For further info on how the game engine treats different locations depending on whether the player is nearby or not, please see this page.