Your microSD card is 64 GB in size.
You can access it all if you follow the instructions to expand the file system.
The eMMC is 4 GB in size.
If you need less than 4 GB, then you can use the eMMC.
If you do a lot of writes, then the 64 GB card will last much longer, since the write leveling algorithms have more memory to work with.
If you are just using the BBB for learning and experimentation, then you will never use it enough to worry about wearing anything out.
With the uSD card, you could have several different cards, with different programs or operating systems on them, and easily switch back and forth.
So, as usual, the answer is "it depends on what you want to do, and what you care about."