Unless you run into problem filing through PS, you would normally not want to file directly with BSA.

The biggest advantages of filing direct is that BSA does all the validation for illegal characters before submission, it doesn't matter if the spouse is an NRA without ITIN or that your client only has signatory authority without any financial interest in the accounts reported, and you receive the acknowledgement often much quicker (instantaneous receipt and acknowledgement within 48 hours.  The primary drawback is that it only allows discrete filing, which means you have to e-file each FBAR one by one.

So Pro Series supports efiling of the FinCen form 114?  Everytime I check on the efiling status it just says that the federal return has been accepted.