Short version: Internal stuff, complicated. Just use myisam
Long version: The engine is how the database internally stores things. Each MyISAM table is stored on disk in three files. The files have names that begin with the table name and have an extension to indicate the file type. An .frm file stores the table format. The data file has an .MYD (MYData) extension. The index file has an .MYI (MYIndex) extension. For more on the engines, go here MySQL AB :: MySQL 5.0 Reference Manual :: 12 Storage Engines

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