So the IV are kinda like merit points put into stats? If you have "31" but you are only level 10/100 you only get a % of the "31" applied?
Correct.
There are 4 sets of stats. IVs, EVs, Natures, and Base Stats.
Base Stats are all static to the family. What one Charmander has, all Charmanders have. But Charmander and Squirtles have different Base Stats. So do Charmanders and Charizards.
Natures affect the stats by taking the Base Stat and multiplying by 10% up or down depending on the Nature. You can see what stats are affected by the shade of the words on the stat screen (Red being +10%, Blue being -10%). Neutral natures are those who affect the same stat twice (Att+10% and Att-10%), meaning that they net each other out. Remember, it is only effecting Base Stats, nothing more.
EVs (Effort Values) are determined by type of pokemon you fight or, in the case of X/Y, the Super Training you do. EVs work like this: You have 0/255 of each stat, but you can only put like 512 EVs all together, and you can only max 255 in a specific stat. 4 EVs in 1 stat = +1 stat @ 100. That means you can increase your total, level 100 stats by +63 (system rounds down, so you can't go higher than +63). Obviously this is the most important way to boost stats. This is the only way to change the stats of a Pokemon.
IVs (Individual Values) are determined by the actual capture or breeding of a Pokemon, and are set in stone after you first meet them. The max IV you can have on any stats is +31. But, you can have +31 on
all stats. It used to be very rare, but now it just takes work to get +31 on all stats, due to breeding.
So, if you plan it right, you can add up +10% of a base stat of a Pokemon + and additional +94 on a specific stat. That can be a huge boost when fighting other players.