You just buy a good RO/ID system. You only need one system. You are only going to fill up a 1000 gallon tank once. So you don't necessarily need a set-up that will put out 1000 gallons in a hurry. After the initial filling, you will be doing something like 100 gallon/week water changes. You will also want some water storage tanks for a system this big. I'd say at least one 100 gallon tank. It would be best to have about 300 gallons or more worth of water storage just in case you have an emergency that requires a large water change.
Buy whatever you can afford... of course a unit that is rated 180 gallons/day will put out twice as much as 90 gln/day unit. Basically it will take about 10 days to fill the tank with the 90 gln/day or 5 days for the 180 gln/dy unit.
You would definitely fill the tank with water first, then slowly add salt.