Unfortunately, X.A.N.A. also knew how the way towers worked and in Season 3, he used the Scyphozoa to possess Aelita and then guide her to the way tower, once inside, X.A.N.A. would take her to the upper platform where she would enter, Code: X.A.N.A., this would give X.A.N.A. complete control over the sector and he used this procedure to delete the sector for which the code had been entered.
In Season 4, Odd discovered that regular towers have the data streams running below their platforms however jumping into them would only send you back to the tower the person jumped from or to another tower in the same sector. Also in this season, William being under the control of X.A.N.A., could type in CODE: X.A.N.A..
Before Lyoko was destroyed by William in Final Round, the Way Towers were connected with Carthage through wires. But after Lyoko was recreated, it seems that the Way Towers are connected with Carthage using wireless technology. However the normal towers are still connected with the Way Towers through wires.
Since tower locations can move somewhat, way towers are no exception. The Ice Sector's way tower has been recorded in several different locations. Additionally, it appears that the functions of a way tower can jump between towers; as in, on one day, tower A might be the Way tower for the Mountain Sector, but on day 2, it might be tower B.
Way Towers were seen in all 4 of Lyoko's initial sectors, with Carthage lacking one for some reason. However, it's unknown if replikas possessed them or not. This lack of understanding extends to the Cortex and Volcano Sector.