Regardless if I'm doing 3 or 5 AEB I still shoot 5 shot AEB, it's better to have to much data than not enough, but not a huge difference in processed 3 or 5 in my opinion, but I feel the sky comes out better when using 5 shots. I go from Lightroom, to photomatix, back to Lightroom and finish in Photoshop. Its very important to correct white balance, change lens correction and make sure the detail slider bars in Lightroom are set to 0. I think default is set to 25 sharpening. Set noise/color to 0. Once I make those corrections from Lightroom I process in photomatix, then I bring it back into LR and do my slider editing. Then I send it to photoshop to crop, make small adjustments and save.