HelloWorld,
This is not an easy question so I don't have any easy answers. Nor am I the most qualified person on this site to make recommendations. However, I do own a Hsu VTF-2 sub that I am very happy with, and I have heard the Axiom M3ti's, which are very nice for the money (I find them a little bright, but it is a personal taste thing). There will be a significant difference between a system using a bookshelf and a sub vs a full range floorstander. Bookshelf and sub will go lower, but it takes alot of tweaking and fooling around to get them to sound right together. The floorstanders will not have the integration issue, but will not go as low either. Typically it is cheaper to go with a floorstander than a similar quality bookshelf/sub combo.
I see you are looking at an NAD integrated. Nice for the money also. I am using an AMC 3050a and am happy with this "mid-fi" piece as well. Will you require a source? If so you will find it hard to hit your budget and get into a source, integrated, bookshelf/sub combo and connections.
I don't know anything about the Athena speakers so can't comment on how they would compare to the Axiom/Hsu combo, but will say this; I prefer bookshelf speakers in general (imaging especially) and would say that you may want to start with an integrated, bookshelf speakers, source and connectors first. Then see if you really need that low end, and if so, purchase a sub later on.
Just some thoughts,
R