Ah, fond memories of Se-Al.
Define "huge alignments"...?
BBB is made for long sequences (poxvirus genomes = 200-300kb, perhaps a dozen or two), it's not made for 1000s of sequences, even if they're small. Just tried to load 1000 1kb sequences, it loaded after about 30sec and it allowed me to scroll around and edit the alignment. Not sure if the alignment tools would crash if I tried to align them. Just aligned with Muscle... quick to align, very slow to import aligned data back to BBB. So better to align first.
BBB has a variety of unique features, so it depends on what you want to do with the alignment.
We use it for GenBank files of poxvirus genomes, so it knows about annotation of genes.