Which alpha Hydrogens are more acidic?
I was under the impression that acetoacetic ester has more resonance structures so it more acidic. 


That's actually wrong. Deprotonated acetoacetic ester has structures where electrons are donated from ester oxygen into conjugated system. This, while stabilizing system as a whole, lessens effect of electron donation from deprotonated carbon. Think about it this way: carbonyl oxygen wants electrons. While in acetylacetone electrons may be harvested from deprotonated carbon only and in acetylacetic ester they may be harvested from both deprotonated carbon and ester oxygen, stabilization effect in the first case is higher. 

It is well known, that stabilization effect on acidity of nearby $CH$ grows in row
$COO^- &lt; -CO(NH_2) &lt; -COOR &lt; -COR &lt; -CHO &lt; -NO_2$

The more electron deficient the conjugated system is, the more stabilized carbanion becomes, thus the less resonance structures with transfer of the charge onto carbonyl oxygen the group has, the more it stabilize carbanion. Thus, $\alpha-CH$-acidity in carbonyl compounds correlates with electrophilic activity.

The reason is that negative charge from deprotonated carbon must be delocalized as much as possible, which is especially easy with strongly electron-accepting groups. In case the compound already has an electron pair conjugated with carbonyl group,  this is more problematic.