In the right door by the oven, there is a bathroom that is never seen. The Upper Stairs lead to Alex, Justin, Max, and Jerry and Theresa's rooms. Max's room is seen in Report Card in Season 1. Justin's room is seen in episodes, Monster Hunter and in Franken Girl in Season 3. It was also seen in Wizards of Waverly Place: The Movie. Alex's room is seen in Hugh's Not Normous in Season 2. Theresa and Jerry's room were never seen. The upstairs is shown rarely.
Before the series
After Theresa and Jerry married, they bought the apartment where the Russo siblings would grow up. It's possible that they would later add the stairwell into the Sub Station and that at some point the lair had been created, by Alex's great grandfather, though it's not known who charmed it.
As the Russos spent most of their time in the lair or the substation, the loft is seen during the Russos free time. It was in the loft that Max gained his full powers (and maybe his siblings also). However, after Alex wrongly fell in love with herself after drinking a love potion, Justin gave the hat to neutralize the potion's side effects (it made her head grow to epic proportions) Max's unstable full powers began to summon food from the four corners of the world.
In season three Mason came to dinner with the Russos but, he abruptly left, which made Alex suspicious. It would be in the loft that the Russos would come to know about Mason being a werewolf. It was also here that Alex decided to expose wizardry to the world in the Alex Tells the World and that the Russo found out that an asteroid was lurking towards the Earth.