Where/how does innodb store tables in files?
The setting is innodb_file_per_table, and it's default 0 (ie. use one big file) up to MySQL 5.1, and then in either 5.5 or 5.6 the default changed. Changing this value will not affect tables which already exist.  

Even with innodb_file_per_table set to ON you still need the shared tablespace file (ibdata1 file by default).  

There is no one recommended setting, it depends on your databases. Some advantages:
- It's easier to reclaim space from the file (you only need to reimport one table)
- It can be faster on ext* filesystems as they use inode level locking, and so splitting the accesses over multiple files will be alleviate this a little  

Some disadvantages:
- It takes more space, as reclaimed space can only be used in the same table
- It takes longer to recover from an unclean restart
- It can be a big problem if you have a large number of tables (as you can hit an open files limit)
- I might be wrong with this one, but if the temporary tables aren't in the system tablespace a drop table can take a long time  

What problem are you trying to solve?