Feh, sometimes the mechanics are better demonstrated than told, honestly. Said the guy who rewrote the rules just for Ruby and Sapphire... OK, first off, there is no Level bonus in a typical sense: Your level determines how strong the Type and Evolutionary bonuses are. Higher levels mean more severe Type Bonuses.

Type Bonuses are basically calculated thus: If I were to use a Rapidash against a Chikorita, that's 1 type bonus: Fire beats Grass. If I were to use the Rapidash against a Paras, that's 2 type bonuses because Paras is doubly weak to fire. If I were to use a Charizard against a Chikorita, that's ALSO two type bonuses because Charizard has two types that Chikorita is weak against. If Charizard went against Paras, that's FOUR type bonuses because Charizard has two types that Paras is doubly weak against. Resistances/immunities are completely ignored in GCeA, for the record: If we didn't, steel would be OP to the max.

Bonuses work very differently if you're trying to capture or battle a Pokemon: Wild Pokemon can't have points taken from their totals if you're trying to capture them. They ADD Points to their totals if THEY get bonuses against your Pokemon if you're attempting a capture, and never the other way around, but if your Pokemon isn't inferior to them in either sense, it's just the cost listed. As higher point costs mean you must pay more points to get said Pokemon, well...It's a good idea to not have the Pokemon stack up bonuses against you during capture.

On the other hand, if you want to battle the Pokemon rather than catch it, it's a different story: ff you're trying to battle them, you're affected by their bonuses still, but they can also be affected by any and all bonuses you can press upon the enemy Pokemon, which makes them go down. Negative Bonuses are the GOOD kind of bonus, as all bonuses are applied to the enemy Pokemon, and the shorter the point totals, the faster they go down.

I hope that will suffice for an answer. :P I'll be happy to attempt to rephrase it to make it more understandable, if that's OK.

On the topic of this OP...What's an OP? :P Sorry, I'm unfamiliar with the term used like you used it.