There are several checkboxes that you can mark, mark everything that you plan to use.
For example, if I was SRing for an egg then I wouldn't need to mark nature, ability or gender because the egg is already locked with those characteristics. In that case I just check the boxes for every IV, input the range of IVs I want for every stat and the IVs of the parents, hit the button "Begin Calculation" and check out the outcome.
If you are mass hatching then you should check the nature box, select if you are using an everstone, mark the gender box if it matters to you for some reason like the male parent is good already but the female is only double flawless so you want to know your chances of getting a female, finally check the IVs and fill the desired IV ranges and IVs of the parents.
It's not very intuitive but it isn't that difficult to figure out on your own either.