I'll explain in an example:
The spell I have is Shock Damage 10pts and Weakness to shock 100 pts for 10 secs.
Basically it means that the Shock damage WILL NOT be amplified the first time the spell is cast, so the target will receive 10pts of Shock Damage, as well as the weakness spell. The second time it is cast, the damage would be amplified 100%, so the target would be hit with 20 pts of Shock Damage.
To make a long story short, a damage effect will not be amped if it is with a weakness effect. The SECOND cast would be amplified, not the first, assuming that the weakness is still in effect.