If you want to play it safe with changing a table to InnoDB, I have a nice suggestion:
Create a new table as InnoDB and load it
For this example you have a MyISAM table called mytable in the mydb database. You can perform the following:
use mydb
CREATE TABLE mytable_innodb LIKE mytable;
ALTER TABLE mytable_innodb ENGINE=InnoDB;
INSERT INTO mytable_innodb SELECT * FROM mytable;
ALTER TABLE mytable RENAME mytable_myisam;
ALTER TABLE mytable_innodb RENAME mytable;
That's it. The new table is InnoDB plus you have a backup of the original table in MyISAM with its original contents and layout. You are free to perform whatever other conversions you need on the new InnoDB table.
CAVEAT
Make sure you optimize InnoDB
InnoDB performance tweaks
Howto: Clean a mysql InnoDB storage engine?
How to Safely Change InnoDB Log File Size
Major Differences Between InnoDB and MyISAM