In principle, the 49ers run a 3-4 defense, however, teams without a strong running attack rarely see it. In the absence of a serious running threat it morphs pretty quickly into a 4-2-5, 3-2-6 or 4-1-6 defense.
The 4-2-5 is the nickel, with Ahmad Brooks and Aldon Smith as the edge rushers and Ray McDonald and Justin Smith as the interior lineman. Bowman and Willis, the fearsome and well-known interior linebackers are the 2, and the 5 DBs include safeties Whitner and Goldson, and cornerbacks Carlos Rogers, Tarell Brown and Chris Culliver (2nd year). In the dime defenses add Perrish Cox, who is new to the niners this year and seem to be a real upgrade in the 6 DB formations.
Personally I think Stafford is one heck of a quarterback and with a target like Calvin Johnson, well that is a tough challenge for any defense. I am not really sure how the niner secondary "contained" them last year, if holding a receiver to 120 yds or so counts as containment, but presumably it involved a lot of double coverage with right corner T Brown getting help from Goldson, Whitner or Willis.
The thing that has impressed (and surprised) me is that a bunch of guys who are mostly around 5'11" (on a good day) can defend a guy who is 6'5", fast (and strong). My guess is that we will see mostly pass defenses with both Willis and Bowman on the field due to the size/height challenge that CJ presents.
GB saw 7 snaps of base 4-3 last week. I am thinking that you (Detroit) will see a lot of the same defenses Green Bay saw from the niners last week and very little base. Does that seem reasonable? I would roughly put the over/under at 10 snaps in base, with the rest nickel or dime pass defenses. (Feel free to pick under or over and explain/defend your pick if you like.)
I think the 49ers win this because it is not that easy to pass into their 5 and 6 DB defenses.