I too have issue with the way the alignment tool functions. It would be great if you could do a three point alignment like in AutoCAD, but you can also use the translate tool and get close to the same functionality.
I also have a thread regarding align here with some tips and tricks. I would start by watching this alignment video and then the translate one.
Translate has become my go-to because after you choose the object you want to align, you can then select an edge and continue holding the mouse button to snap to a specific point.