You absolutely need to keep a few things in mind:
+ If your software users MyISAM specific things such as UPDATE LOW_PRIORITY or INSERT DELAY these do not work in InnoDB and it will break your software.
+ Converting really large tables via ALTER TABLE is not always a good idea (see later for a better way)
+ The size of your database, around 20GB, isn't actually that big and with 64GB RAM, you should have instant queries on everything, so if there is latency issues you probably don't have correct indices. Unless, of course, there's a lot of UPDATEs which happen, then you can benefit from InnoDB's row-level locking.
But to answer your questions:
+ You do not need to convert them all at once, you can easily have a mixed database of different engines
+ Performance options don't really exist for converting tables
I recommend you...