This question has been answered in part here: PCA first or normalization first?
To answer your questions directly:
Normalizing would be a personal choice. If you set centerData=TRUE, and do not normalize or standardize your data, some attributes with large values will have greater influence in the PCA. If you set centerData=FALSE, Weka standardizes the data for you.
And just to confirm your suspicions, in Weka, centerData does the following:
centerData=TRUE
- Centers your data (does not normalize or standardize, so if you decide to do that, you need to do it before)
- PCA is performed with the covariance matrix
centerData=FALSE
- PCA is performed with the correlation matrix (data is standardized by the method)