I have been pondering this myself. My kid's car seat is in the center of my crew cab. The anchors are there to accommodate. I wanted to revisit this though because I thought I remember reading in the manual something about using the sides. I don't think it said specifically to only use the sides, but it made mention of the anchors being located there without mentioning the center seat. That being said, three car seats can be accommodated in the back, so I do not think by design any one spot is safer than the next. While behind the driver and passenger gives you a few more inches of seat bottom, the middle places the child in what is likely the safest zone, taking into account you do not know where you will be hit. The sides are great if you only get hit on the opposite side.
Furthermore, I do not know how the side passenger airbags deploy in the rear, but airbags are not always the best thing for someone as small as a child.<-- This bit was paraphrased from the American Medical Association's and GM's 'Protecting Children in Motor Vehicles: A Matter of Restraint' pamphlet. It is a bit dated, but still relevant.
Lastly, what was the suggested placement of car seats in the old Dakota extended cab? Or even the current Toyota Tacome ext. cab? If I recall correctly, those accommodate car seats but the seat cushion is not big enough for the whole base to sit on. I would think this again suggests that, to a certain extent, the size of the cushion does not matter.
Perhaps the best solution is to call Chrysler or ask your dealer. Without someone to say definitely, it is all opinion and preference. I have to get with my dealer in a day or two, I'll try and remember to ask him.
Keep those little ones safe!