I just finished both 12-week programs a few days ago. My split looked like this:
Monday: Upper (Chest)
Tuesday: Lower (Squats)
Thursday: Upper (Back)
Friday: Lower (Deadlifts)
I’m pretty sure this is how it’s supposed to be. However, Ian does say that you can get away with only doing one legs day. If this is the case, you might want to combine 2-3 of the key lifts from both the squat emphasized and deadlift emphasized days. Just make sure the set and rep schemes fall within the 3-week phase you’re in.
Recovery wise, I had no problem. In fact, I saw my best results in Squats and Deadlifts. However, if you’re still nervous about recovery, I’d do what james_526 said and take a week off after every 3-week phase or every 6-week phase. Ian acutally recommends doing this in his later programs.
Personally, I used this program right after running a marathon in late May. The first three weeks of this program were great for me because they eased me back into weightlifting, and by the last three weeks, I’d regained almost all the strength I’d lost during my three months of training.