Hi, Sungjin-
Well, as long as your EPI and anatomical dsets can be aligned, what you did is fine. (Was your anatomical dset also acquired with oblique coords, and, if so, did you deoblique it in the same manner with 3drefit?)
I would not recommend just applying 3dWarp -deoblique to your EPIs before processing, because that will resample your dset, which is a smoothing process. afni_proc.py should be able to deal with all of this internally, only perhaps needing an option or two for the "align" block-- but were you having trouble with EPI-anatomical alignment?
12 GB for processing sounds reasonable to me... what is your EPI voxel size? Actually, what is your afni_proc.py command?
--pt