I'd put each one in it's own schema so that no two companies have to worry about their data showing up on each other's site. the closest thing to a schema in MySQL is separate databases, so I'd use those.
While it might be easier to maintain the schema of your setup with one big table, it's not the best option from the point of view of keeping your customers separate from each other.
Update your schemas with .sql scripts, and you can automate if pretty easily by just running that script against all the dbs / schemas in your server.
Bascially, things that are related should be stored together. These data sets aren't really related, I take it.