I'll assume you have a solid-mounted engine, as in a Shovelhead or Softail Evo. The proper alignment being talked about refers to the engine and transmission being alighed with each other and in the frame.
First, the top engine mount should be snugged to the head, not tightened yet. Then check the space between the mount and frame. Insert enough washers to just fill the gap without pushing (loading) the mount in either direction. Now tighten the center bolt. Then finish tightening the nuts on the heads. If you load the top mount to either side, excessive vibration and broken engine mounts will be the result.
I have a Harley-Davidson, and was wondering what is the correct method of installing the top motor mount? What I've read says use proper alignment of use some shims that were originally installed. Won't the torqued mounting nut tend to pull the top end over just a bit?