When a figure such as IG-88 is on the board, are passive bonuses used?

Examples: When attacking IG-88 do you add his +1 do defense? When IG-88 attacks does he always get his +2 accuracy if it is not shown in the "Bonus" box on the app / does the bonus stack with his passives.

When IG-88 Attacks does he still receive Arsenal, Relentless, and Assault abilities or does he only get them on turns the app specifically says he does?

We have also been playing that the Surge priory list always overrides surge abilities listed on the card.

Yes, all mandatory bonuses and abilities are used. Only the abilities with "may" or "choose" are ignored.

Click the deployment group and the Info icon to see which ones should be ignored.

Arsenal includes a choice, and the app should say which dice to use for each activation. (At least I remember it doing do.)

Relentless and Assault are mandatory and are in effect.

Surge priority is only showing the order to apply the surges (but it should have the same abilities listed as the abilities on the card). Note that if a surge ability would not change the game state, you skip it. (So, a surge for a condition would not be used if the attack does not cause the attacker to suffer damage. You spend the surge for damage or pierce instead.) If any surges are left over, start the list from the beginning.

Yes, but +1 to defender I always forget it.