There are two tables and their default engine is InnoDB.
I want know the following
- What's inside the ibdata file ?
- How does InnoDB store these two tables ?

Percona created this picture a long time ago. As you can see, ibdata1 contains many classes of data structures. There are as follows:
If you are concerned how indexes are stored, please read my earlier posts about InnoDB indexes
Apr 04, 2012 : How does innodb_stats_on_metadata relate to query execution plan stability?Jun 28, 2012 : Benefits of BTREE in MySQLOct 26, 2012 : How badly does innodb fragment in the face of somewhat out-of-order insertions?Jan 09, 2013 : Is ANALYZE useful immediately after creating an InnoDB index?Mar 27, 2013 : Are there implicit indexes in InnoDB like MyISAM?Jun 14, 2013 : Does the size of the primary key contribute to table size?