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How do you use the markings?

I use them for marking perfect IVs. I have set boxes for breeding, some for wild captures, some for those I want to keep. Using it to mark IVs help a lot if you breed and trade Perfect IV Mons
 
I use the marking for my party members.
 
In Diamond, my system was:
-Circle for pokemon that I need the pre-evolutions for the dex, representing an egg shape.
-Triangle for pokemon that I need evolutions for the dex, representing an upward arrow
-Square to easily locate pokemon with Pokerus
-Heart shape for traded pokemon
-Star for EV trained pokemon
-Diamond shape for shinies

As of XY, I just use them for IVs though.
 
Alot have mostly started using them to signify a Perfect IV stat it has in, and if you haven't, you really should. It could help you and other people who you trade some Pokemon to.
 
I use them to mark down my Pokemon's perfect IVs, now that I actually do IV breeding in Kalos.

In B2/W2, I used the heart marker for my favorite Pokemon, as in the ones I trained or planned on training; the star marker for special Pokemon, like N's Pokemon for example; and the diamond marker for Pokemon with their hidden abilities.
 
I never got the purposed for the markings so I've never did use them. Probably won't in X and Y though they seem good for organizing.
 
I pretty much only play the games for quick play-throughs and/or challenges so more often than not I don't actually bother with the markings.
 
In previous games, I would use the heart marking to denote my main party Pokemon.

Now that I've started IV breeding, I've realized how unbelievably useful they are for remembering which Pokemon have perfect IVs in which stats.
 
I've used them for marking perfect IVs since at least Platinum, because other than that I never really saw much of a point for them. But they could be used for conveniently marking specific stuff of yours I guess.
 
I never actually mark my pokes and I just went thru the game since I don't trade and only care about is Pokemon's EV stats
 
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