Hey Starbug,
APC does not need to be enabled in vBulletins config, none of the cachers do (although it is recommended so their datastore is cached). That said the only config I do read is memcache connection values if you use Memcache (again though, It doesn't need to be hooked upto the datastore).
As for the prefix, they do not have to be the same. The option for the prefix in vBO is given incase you run multiple installations of vBulletin on the same server (or using the same memcache server) so cache doesn't collide.
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