Two months to get from Santiago to Buenos Aires? Brilliant.
You could basically choose to 'do' the south or 'do' the north west. Seen that you're going in September, I'd definitely pick the north west: south is really quite cold that time of year. Two basic popular north routes: via Mendoza (Argentina), or via San Pedro de Atacama (Chile). I your case I'd pick the latter, and go:
Santiago - San Pedro de Atacama (with stops in between; I don't know that part of Chile very well, so best ask others) - Atacama desert -
from the Atacama desert, you can cross into Bolivia to see the salt plains (with a booked tour), or into Argentina directly (regular bus service). I highly recommend the salares. Assuming you'd go that way, the itinerary continues
Salares de Uyuni - Uyuni - train/bus to Villazon (border with Argentina) - Jujuy - Salta - Tucuman - Catamarca - Rioja - Cordoba - Buenos Aires.
You should consider making one additional stop in Bolivia (Tupiza, which is really nice), and as many stops as you like in the rest of the trip of course.
General tip regarding Argentina: the central part is skippable. Cordoba and surroundings is very beautiful, but the entire rectangle between Cordoba, Rosario and the Paraguayan border is generally considered somewhat boring. If you need more specific information, do ask.