How do I know if the bonus was applied?

The text in the mod says +2 Spark:

but when I check the Lilith Skills tree, the points are the same (I added those 3 points there, they were not added by the mod):

How do I know the bonus are working and the values are counting as they should?

Shouldn't it show 5 in Spark???

Solution 1:

It will not indicate your class mod bonuses on the skills (they fixed that in the later games). But it will still calculate it in! That means you have to trust the indicator on your class mod description.

I remember that from playing the game for about 300h, but I just went ingame to confirm. Used a Hunter class mod that gave me +2 on the Caliber skill, which increases your sniper rifle damage.

Shot a random enemy a few times without the class mod: 317 damage
Shot the same enemy a few times with the class mod on: 335 damage

And I got no indication in the skill tree. Also my skill was maxed at 5/5, so it was actually calculated at 7/5.