If that is same calculator I have downloaded before (I did not open your link, but appears to be the one on Mike Holt's site, which I have downloaded before) it will not accurately give you load side results of a separately derived system. You can start from the top at the separately derived system - but it is going to assume infinite capacity from the transformer input, which will leave you with a higher then actual result. Many times that works, but when you get to the point where you are on borderline of one kA rating or another from your equipment it can be a costly decision made if you choose not to have more accuracy.