There is a word for what Warren is...but I'm not sure I'm allowed to use it on the forum...
yes, he is a genius in the area of technology, clearly. And honestly, he is not nearly as socially inept as his partners, he shows a reasonable amount of savvy, even if he is that word I'm not allowed to use. Of course, once his character got interesting, the writer's play with it to suit their needs, so Warren does not remain consistent, he changes in order to keep him around and keep moving the story forward.
I often wondered why he didn't take his very real skills and get money and recognition the honest way. He could have been a billionaire, but then, where would the humor and evil that he brings to the show be if he'd taken that route?
There are levels of characters on the show (on any show), and Warren is in a level where you have to allow more leeway and flexibility, don't expect everything they do and are capable of to totally mesh with each other, they are less characters we are supposed to identify with and more vehicles for plot development.
So, he can be an idiot and genius both, whichever meets the writer's needs at the time, and we are not supposed to press too hard for the loose ends to be tied up.
The best explanation I can think of for his hiding his skills in a basement and using them to take over a little town like Sunnydale is that the formula is taken right out of comic books, it's a nod to them. In comic books you have all these geniuses who work late at night in their basements with plots to take over...something. It's the genre. In that sense it fits the characters and their "nerd/geek" identities. Since they were little boys, they've had some fantasy in the back of their minds to play out a dark dream.