A character's effective skill is their skill level taking into account all the modifiers which apply at the time. Sometimes this will be the same as their basic skill level. Hand-to-hand combat skills are probably the most common example of this.
For example, if someone has a Broadsword skill of DX+1 and 14 DX, then their basic skill with the broadsword is 15. Most of the time they will be using a broadsword in a fight without any modifiers: they are standing within a yard of their opponent and making one attack and one active defence each round, not trying anything 'fancy'. In that case, their effective skill is the same as their basic skill: 15.
But there will be times when the player will choose to do something different. Let's suppose Lancelot finds himself in combat with Sir Gorlois, a heavily armoured opponent with a decent skill level. After a while, it becomes clear to Lancelot's player that even when he does manage to get a hit past the opponent's shield, the armour is taking almost all of the effect out of his attacks.
The player decides to do something a bit different.
He declares that he is about to do a feint in the next round of combat, then follow it up with a targeted strike to his opponent's weapon hand. In the turn where Lancelot feints, he does well enough to win his Quick Contest of Skill against Gorlois' Block skill by two points, giving him a +2 to count against his attack next turn.
In the second turn, Lancelot still has his broadsword skill of 15. But he gains +2 to that because of the effect of his feint last turn. Then he needs to take a -4 penalty to strike the hand because it is a small target. His effective skill, therefore, which is the number he needs to roll against, is (15 +2 -4) 13.
A more common example is in ranged combat. Deadeye Dick might have a skill of 18 with his six-gun, but that's only the number he rolls against if he is shooting at a man-sized target within two yards. When Putrid Pete calls him out in the street at High Noon, Dick's chances of hitting aren't that high.
They face off at about twenty paces, and at Putrid Pete's first twitch Dick needs to clear leather and blaze off his first shot faster'n a scalded cat. He has no time to Aim, and intends to duck the moment his shot's off [that's keeping the option of a Dodge open, so he can't do All-Out Attack]. He has no advantageous modifiers, but there is that twenty paces' range – possibly a little less than the full 20 yards, but certainly more than fifteen, and that's a -6 modifier.
Deadeye Dick's effective skill, then, is the number he needs to roll against in that circumstance: (18-6) or 12.