Online Documentation
MySQL
Table engine
You can set created table type to InnoDB (transaction-enabled) or MyISAM (non-transaction type). Each has it's advantages and disadvantages, for more details please consult MySQL manual.
When you use MySQL as both source and database (upgrading or doing scheduled backup for example), Full Convert copies original table engine of each table to allow your customizations to be preserved. If you would like to force a specific table engine when copying, check appropriate checkbox.
Misc
When specifying MySQL connection, you can specify default pre-filled username so you don't need to type the same value every time. Default is "root".
Forced index length specifies index column length which is enforced on indexed blob columns when index length for such column is not specified. Typical scenario is converting a very long varchar column that ends up as text column. Source varchar column was fully indexed (not only a beginning of each field). For blob datatypes, MySQL requires length to be specified - so we force only first n characters to be indexed. This can result in exception if source index was unique and target is not unique in first n characters. In such cases, increase forced index length to a value where this does not happen. Do not exaggerate as index could grow to a level where it hurts performance.