It means add 533 grams of DME to 5 litres of water - this gives you a wort of approx 1.040 SG which is good for hop utilisation - and bring to the boil.
Use the HCF, adjusting the boil volume will alter the amount of malt required to hit the above figure and you will notice a difference in hop utilisation, resulting in a change in IBU. Better hop utilisation = less hops required.
Your hop additions are all made in the boil which can be strained at flameout and the hot liquid used to dissolve your LME's and remaining malt in the fermenter or it can be cooled in an ice bath (covered) and carefully poured, to leave the kettle trub behind, into the malts already mixed and dissolved in the fermenter.
Of course, if you have the capacity, you can just dissolve the malts directly in the kettle at the end of the boil and strain/decant into the fermenter, but the sugars caught in the trub (hops and break) will be highly concentrated as opposed to what remains if straining/decanting a ~1.040 wort.
As per your recipe, I personally would be adding another 10 IBU if, in fact, an APA is what you wish to create. As the spreadsheet indicates in column N, you IBU is LOW, meaning it is less than the minimum specified in the Style Guidlines. As is also indicated in the graph. The blue box is an illustration of the Gudline specs for a particular style. Your recipe leans more to the malty (sweet) side than is appropriate for an APA.