Auto layout lets you do things that are very difficult using manual layout, such as "pinning" a view that's inside a scroll view so that it "stays put" relative to something outside a scroll view as the rest of the content scrolls, or making a whole set of labels / views the same width with dynamic content or localization.
Yes for some cases manual layout is the best. For example I recently found myself positioning some labels on the axes of a graph. Simpler to just set the center property in that case rather than trying to set up constraints. But for the vast majority of cases (particularly where you don't have to write code...) I find auto layout to be the easiest way to handle the 4 different iPhone screen sizes automatically.
I think we can all agree the constraintWithItem:... and even the constraintsWithVisualFormat API are, shall we say, messy in code. I prefer to do as much in IB as possible.
Anyway, that argument aside, the OP's problem is most likely in the "i apply the constraints" step. *What* constraints were applied? If you just blindly choose "reset to suggested constraints", well, that will almost always end in failure. Xcode is not a mind reader; it can't know whether you want a view to stick to one edge and remain the same size, or resize to fill the space. You must add constraints yourself so things are positioned and sized the way you want them. (BTW, pasting images into posts does not work. Nobody can see them.)