Generally bonuses stack multiplicatively, resists reduce the remaining amount.

For example, say you have a Burst with with a base hold of 225 m3. The Burst gets 5% hold space per Minmatar frigate skill level. Using my pilot, that would be a 5. So I get a 25% bonus to hold size.

My effective hold would be 225 m3 * 1.25 = 281.25 m3.

Lets say I then add an expanded cargohold II (for an additional 27.5%).

The math works like this: 225 m3 * 1.25 (pilot) * 1.275 (module) = 358.59 m3.

This kind of stacking math lets the industrial ships take on cargos you would never think fit into a base 5k hold. With maxed skills and optimized for cargo, a Mammoth (base 5625 m3 hold) can haul 31000+ m3 of stuff.

With damage dealing mods you often have stacking limitations, so that you start getting diminishing returns. Though your skills don't invoke diminishing returns.

A max skill Jaguar pilot, with T2 auto cannons (and Small Autocannon Spec V) would have a basic damage mod looking like this:

Small Projectile Turrets V 1.25
Small AC Spec V 1.10 (2%/level)
Minmatar Frigate V 1.25
Assault Ship V 1.25

Or 1.25 * 1.25 * 1.25 * 1.1 = ~2.15 base damage before modules.

Cap and shield regen generally don't have diminishing returns.

Resist mods work differently, than all the others, and suffer from diminishing returns.

Without diminishing returns the formula is resists = 1 - ((1 - rmod1)(1 - rmod2)(1 - rmod3))

For example: putting a 50% resist mod on a ship that already has 50% resists would look like this:

1- ((1-0.50)(1-0.50)) = 1- (0.5*0.5) = 1 - .25 = 0.75 or 75% resists.

Lets say we add a 3rd resist mod with a 15% resist mod.

The formula (without diminishing returns) would look like this:

resists = 1- ((1 - 0.5)(1 - 0.50)(1 - 0.15)) = 1-(0.5*0.5*0.85) = 1- 0.2185 = 78.75%