To me 1000 sq feet for 2 bedrooms sounds fantastic. So many ways you can use that space creatively. So many different layout options and shapes.
My recommendation would be to start with an architect. Given a good budget and defined parameters you should get something really good. And (at least here, don't know about there) architects like to be project manager as well to make sure their baby is executed well.
[1] starter apartments here can be under 200 sq feet. Not sure who wants that (they are typically quite expensive) but someone is buying them.