Critical hits with penatilties for damage.

[Catprog]

From http://www.d20pfsrd.com/gamemastering/combat

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Sometimes you multiply damage by some factor, such as on a critical hit. Roll the damage (with all modifiers) multiple times and total the results.

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A critical hit means that you roll your damage more than once, with all your usual bonuses, and add the rolls together.

Does the 2nd rule trump the first? (ie use bonuses and not modifiers)

And if you use the modifier one , is it possible that if you rolled a 6,1 that confirming the crit would make you do less damage then if you hadn't?

[Quantum Steve]

You roll damage twice, including all modifiers (even penalties) and add the results. You can never do less damage with a crit, however, because you can't deal negative damage.

For example, say your damage was 1d6-2

Your first roll is a 6, so 4 damage.
Your second roll is a 5, so 3 damage.
Add those together to get 7 damage for the attack.

another example

Your first roll is a 6, 4 damage.
Your second roll is a 1. 1 non-lethal damage.
Add those together to get 4 lethal and 1 non-lethal damage