Markings
>A marking tool was introduced in the Generation III games,
> with Lanette's Pokémon Storage System. This tool helps the player to
> organize their Pokémon within the Boxes, but is not necessary for game
> play. Each Pokémon can be marked with any combination of the different
> markings. Prior to Pokémon Black 2 and White 2, this could be done
> only while the player was operating the Pokémon Storage System. In
> Generation III, there were four markings: ●, ■, ▲, and ♥. In
> Generation IV, two more markings were introduced and the existing ones
> were reordered, making the full list ●, ▲, ■, ♥, ★, and ♦, in that
> order (this order is kept in all later generations). The markings
> appear in the Pokémon Storage System and on the Pokémon's summary
> screen. A Pokémon will keep its marking settings if traded to another
> Trainer.
Taken word for word from here. TL; DR: Markings don't do much bar making organizing easier. I know that many people use the symbols to denote 31 IV stats on bred Pokemon, to mark out the best for competitive.