There are several ways they could go.
I think there are three potential directions: Offensive Line, QB and Running Back.
There are a lot of good receivers still out there.
So if Ryan Mallett is available at #41, I think you have to go for it. He's the one player that most of the draftniks believe has the talent to be a franchise QB. However, there is the risk of a Jeff George type of guy. Skins don't need another #3 car. However, I think the Shannies would be a little more patient with their own guy. Marty had no patience for JG but there was very little that Marty had patience for (particularly short owners). I think Dalton will be gone. Kaepernick could be there but he's a longer term project.
On the offensive line, there aren't many guys who grade out in the 1st half of the 2nd round. If Mallet is gone, could they trade the pick and pick up a 3rd rounder to move back in the 2nd. It looks like Kaepernick may be falling in this draft. Skins could take Kaepernick at 49 and pick an offensive linemen later in the 2nd and another one in the 3rd (if they trade down again).
3rd option: Running Back. Mallet at 41 and Ryan Williams or Mikel Lashoure at 49.
Prediction: Skins go for Mallett if he's available at 41. If he's not, they will draft a one of the running backs at 41 and a Offensive Lineman at 49.