For your "main" question, you will have to take your first steps into EV training. Here's Serebii's [link]. It explains everything you need to know. Additionally, knowing about [natures] would be of great help as well.
Take time to understand it. Not everyone gets it in one sitting.
As for your movesets, I'd highly suggest replacing Dragonite's Dragon Pulse with Outrage, and Fire Blast with Fire Punch or ThunderPunch. Fly also makes him quite predictable... Roost may be a better choice instead.
For Arcanine, remove flamethrower and teach it something else non-fire as you already have Flare Blitz (which is physical). Thunder Fang may also be replaced by the superior Wild Charge (i think this one was Gen5 though, so you might have to ask someone to teach it for you). Will-o-wisp, Hidden Power Grass (to get rid of Water/Rock/Ground types that attempt to kill you in one shot), or even a Sunny Day+Solarbeam combo could work well with him too. Not to mention Sunny Day, aside from boosting your Fire attacks's power, could aid your Shiftry as well (skip next paragraph if you want to immediately know why).
For Shiftry, focus on physical attacks instead (get rid of everything, basically). Teach it Seed Bomb (move tutor) instead of Energy ball. Sucker Punch, Synthesis (both from tutors as well) and Swords Dance(ask someone who owns any Gen5 game, preferrably from this site's Trade Corner, to teach it via TM) would make him much much more of a formidable opponent.
However, if you really want to persist with your (Shiftry's) current moveset, you may remove Leech Seed and teach it Nasty Plot instead. Giga Drain instead of Energy Ball is quite good with Nasty Plot, too. Regardless of your choice, make sure your Shiftry has the ability: Chlorophyll too. This doubles his speed under a sunny weather (caused by pokemon with the move: Sunny Day, or ability: Drought). And while it's sunny, you could spam some Solarbeams(special attack) as well. In this case, remove Shadow Ball (not really gonna be useful for you, since Dark Pulse is already effective on both Psychic and Ghost)
Try to focus each pokemon on having a moveset consisting of just one type of attack first:
Physical (raise attack); or
Special (raise Sp. Attack)