I have noticed several places where the person has grouped all the parts needed into one or two 8x8 STL's.

Is there an easy way to ensure that the parts all line up on a common plan?

Which software is best to use.

So far my attempts have not been very successful.

I use Repetier Host to load up and arrange all my STL files. From there you can save the group into a single file that you know is arranged for your build plate.