Either method will work.
-- On my older GMC truck the stock 10si alternator was connected from the Bat terminal to the main lug on the starter, with a fusible link, and then the large diameter positive cable ran from the main lug up to the battery.
-- When I switched to a higher 94 amp 12si alternator I ran an 8 gauge wire directly over from the alternator Bat terminal to the battery positive, and added the right size fusible link. I like this setup because troubleshooting is easier. It also works well for my application because both battery and alternator are on the passenger side, so the cable is short.
-- On some newer GM trucks (mid 90's), a direct wire from the alternator to the battery was the factory setup.
Bruce