You seem to be missing a key concept here: directory synchronization and Exchange hybrid configuration are not the same as the actual mailbox migration.
In order to migrate mailboxes you need directory sync and an Exchange hybrid environment, but then you will decice which mailboxes will be migrated and when; it's perfectly fine to keep some mailboxes on-premises and some other ones online, even indefinitely.
Regarding your questions:
1) Yes, you can limit directory synchronization to specific OUs; but you should be very careful about that: if an object is not synchronized, all Office 365 services (including but not limited to Exchange Online) will not know anything about that object; this means, for example, that a non-synchronized user with an on-premises mailbox will not be known to Exchange Online; that can and will be a problem when on-premises and online users have to interact. Another example not related to Exchange: if you don't synchronize an user or a group, you will not be able to assign permissions to that user or group in any Office 365 service.
2) The Hybrid Configuration wizard enables and configures the hybrid Exchange environment; it doesn't actually migrate anything.
My advice is to synchronize everything, unless you are absolutely sure you don't need specific objects to be known to Office 365; excluding things from directory synchronization can bite you back later in unexpected ways.