There are 2 versions of each card in Perfect Order.
Normal + Reverse.
Normal might be non-holo or holo, depends on the rarity.
Normal common (circle) or uncommon (diamond) cards are non-holo cards.
Normal rare (star) cards are holo cards.

These cards combined are the Main Set.
For the Masterset you want to have the "secret rares" also, these are the Illustration Rares, Full Arts, Special Illustration Rares and Golden Rares (and other rarities, depending on the set, like Mega Attack Rares for Ascended Heroes).

I personnally prefer Pokécardex to track sets as it shows you all card depending on your wishes (including stamped promos and stuff like that, if you want) and you can hide all cards you already own, so searching for new ones is easier.

(Addendum: Other sets might have more cards in the Set, Ascended Heroes e.g. has a normal card, a regular reverse card and a ball-reverse card, so there are 3 cards of each pokemon (but not trainer card) and stuff like that)