How can I store least used table files to a slower drive? Is it possible to separate the least used and most frequently used data files on to separate disks when using InnoDB?
What you are asking is not really an automatic feature in MySQL 5.6, I could be wrong.
Notwithstanding, you can set it up manually.
Given the following information

Your datadir is /var/lib/mysql
You data is in the Database mydb
You have this InnoDB table

Table Description
CREATE TABLE mytable
(
   if int not null autop_increment,
   ...
   primary key (id)
) ENGINE=InnoDB;


You have a data folder to hold the least often used tables called /data/least
Make sure /data/least is owned by mysql  by running chown -R mysql:mysql /data/least

Here is what you must do manually
USE mydb
CREATE TABLE mytable_least
(
   if int not null autop_increment,
   ...
   primary key (id)
) ENGINE=InnoDB DATA DIRECTORY='/data/least';
INSERT INTO mytable_least SELECT * FROM mytable;
ALTER TABLE mytable RENAME mytable_trash;
ALTER TABLE mytable_least RENAME mytable;

How was mydb.mytable manifested before the change ?

The .frm file is /var/lib/mysql/mydb/mytable.frm
The .ibd file is /var/lib/mysql/mydb/mytable.ibd

How is mydb.mytable now manifested ?

The .frm file is /var/lib/mysql/mydb/mytable.frm
The .ibd file is /data/least/mytable.ibd

You should test this out with a blank InnoDB table and make sure.
Give it a Try !!!