If you liked The Atrocity Archives, you'll love The Jennifer Morgue. If some of the more geeky computer references confused you, you'll still enjoy the basic story here (everybody's seen James Bond movies, after all) but again you'll be missing half the fun.
As another reviewer has indicated, to get full appreciation of every little nuance, you need to be an old school UNIX geek, preferably with a familiarity with the Internet that stretches back a decade or two, who still yearns for the days when USENET ruled, and before The Eternal September began.
Not meeting all these criteria doesn't mean you won't find this hugely enjoyable, but the more of them you meet, the more you'll enjoy the book. Having known Charlie since before he'd had anything published and used to hang out in some of the seedier USENET groups, I think I fall fairly firmly into the target audience, and even I missed one or two of the cleverer references first time round. However, I read the book cover to cover in a single sitting and enjoyed every page. Multiple re-reads are a must, the cover's as superb a homage to the book's influences as the story itself, and the story itself leaves an impressive number of openings for more Bob Howards books, from direct tie-ins to the implications of GREEN NIGHTMARE, which Charlie seems to have put in place specifically to give him a way to shut down the Bob Howard universe completely should he ever tire of writing about the character.
Personally, I hope he doesn't tire of writing about Bob for a long, long time. Haven't enjoyed a book so much in years. In fact, although it's a very different sort of book, the last thing I read that established a permanent niche for itself in my mind so quickly was Pratchett/Gaiman's Good Omens in the early 90s. I'm picky about what I read, and I place these two books in a separate little league, all of their own.