Stacking rules govern how multiple bonuses or penalties for the same stat are applied in Pillars of Eternity.
For the exact same stat, a character can simultaneously benefit from...
|category||sources of bonuses in this category|
|any number of bonuses from||weapons||
|one bonus from||equipment||
|any number of bonuses from||passive sources|
|one bonus from||active/modal sources||
Penalties (negative bonuses) are tallied up according to the same rules, completely independently from bonuses - so you could have both a bonus and a penalty from active/modal effects for the same stat.
When a character is affected by multiple non-stacking bonuses for the same stat, only the highest of them is applied, and the rest are suppressed. Their durations still run their course though - when the duration of the highest one runs out, its place is taken by the next highest one that hasn't run out yet.
Note that only the specific bonus in question on the specific character in question is suppressed, not the whole source (e.g. ability/talent) that it came from. If one source causes multiple bonuses for different stats, some of them can be suppressed while others are active - and if it causes a bonus for the same stat on different characters, it can be suppressed on some of them but active on others.
Again, the same goes for penalties.
Multiple stacking percentage bonuses/penalties are added together before they're applied.
For example if you have a 30% bonus and a 50% bonus for the same stat (from stacking sources), the stat in question would be increased to:
value = base × (1 + 0.3 + 0.5) = base × 1.8
value = base × 1.3 × 1.5 = base × 1.95