Create your innodb table after setting the innodb_file_per_table setting (read the mysql manual if you don't know how).
After the table is created, shut the database down, then move the file to the disk you want it to live on. Then use "ls -s /new/path/to/file /path/where/mysql/expects/to/find/it" to create the symlink. Then restart the database.
Try it first to make sure it works.