Is there a difference between an "update" to a scientific paper vs. a "new" paper in a scientific journal?
Recently, I have had a very similar situation occur.  The original paper discussed and explained the theoretical and practical aspects of a scientific technique that we adapted; the second discussed and explained the programming automation of the technique.

My advisor and co-author advised me at the time that each paper has got to be unique, taking the lead from the previous one and adding new information, techniques etc.  The journal that I published in are quite happy to take on a follow up article, just as long as it is sufficiently unique.

So, in answer to your questions - it would most likely be a new paper for publication, make reference to the previous one, but place the emphasis on the new developments.