Example.
An Atlas AS7-D is trying to destroy a really annoying Stinger STG-3R.
The Atlas uses a standard weapon attack. It's Skill 4, +2 for medium range, +2 for the Stinger's 12" Move and +1 because the Stinger can jump = 9+.
The Atlas rolls an 8 and misses. (It would have done 5 damage if it had hit, but it didn't).
The next turn, the Atlas tries again with a standard weapon attack, but using the alternate AC precision munitions. The AC precision ammo itself does not add a to-hit modifier, so it's still the same 9+. The Atlas rolls a 7 and misses again. (It would have done 5+1 if it had hit, but it didn't).
So, the Atlas is fed up with this Stinger, and decides for the next turn it will just use the AC precision special attack. This gives a -2 to-hit modifier (the Stinger has 10"+ Move, so we get the bonus). 9-2 = 7+. The Atlas rolls a 10 and does only the AC medium damage of 2. The Atlas pilot is furious he wasted that roll of 10,but he did hit, and next turn he can use the special attack at 7+ to finish it off.
So the AC precision, when used as part of a standard attack, doesn't provide a to-hit modifier itself, but you still use all the other appropriate to-hit modifiers.
AC precision ammo, when used by itself as part of a special AC attack, does provide a to-hit modifier (assuming the target has at least a 10" Move), but can only deal the AC special ability damage.