How are HP, Defense and Sp. Defense involved when calculating inflicted damage? Like do the defense stats divide or subtract from the attack stats of the opponent and the answer is subtracted from your HP? Is it better to spend more EVs on the defense stats than HP to minimise the damage percentage, or try to get the three values as close as possible?

It's kinda that. There's a damage calculator on the main site, check it out and you'll find out that there are some other values involved, such as level.

It depends on the pokemon and how you will use it. For example, Dusclops and Shuckle have great defenses, but low HP, so it's common that people give them 252 evs on HP.

There's an equation for calculating damage on Serebii

Ah... that's something I've been looking for. Thanks for the link, Sion9!