snpEff with a VCF polarized to the ancestral state

Hi- I'm really stuck on the best way to proceed with snpEff for annotating my VCFs. Prior to running snpEff, I created an "ancestral" fasta based on several outgroups and polarized my VCFs to that fasta. But now, when building the snpEff database, I'm not sure if I should be using that ancestral fasta or my original reference genome. I tried both ways and unfortunately am getting different counts of variant types. So, it clearly makes a difference, but I'm not sure which way is correct. Thanks!