It is assumed that when using skills it is assumed that the character who was trained in the skill, or practiced at it, may (and probably does) knows more about it than the player. So for example when using stealth to creep up on an enemy encampment, a character who knows stealth will naturally do things that the player might not think of as part of the stealth skill, such as cutting branches from a tree and forming a kind of camouflage, and walking toe to heal to augment their silent movement. However, if the player adds to that something out of the ordinary, such as camouflaging themselves with an illusion spell, or wearing special sneakers, or something, then a modifier may be added to the Success Roll. Or, if the player adds something but it is a poor idea, such as placing a chicken on his head, then a negative modifier would be added. Other modifiers might also be added to the Difficulty Level, such as trying to use stealth in broad daylight in the open would give a fairly hefty plus to the Difficulty. So some GM adjudication is required when determining what the character bonus may be for the use of a skill, as well as the Difficulty Level.
On a side note, I recommend that for most actions in the game the calculations be done openly with all modifiers stated before each Skill Success Roll.