There are 2 options you can pick from. (Only number 2 uses JoyToKey so if you absolutely want to use it just skip to there.#1 - Automatic Gamepad controlsBoshy has pre-set gamepad controls you can use (and which you don't need Joy2key for.) To do that, simply go to the 'Options' Menu on the title screen.
Note how next to the controls button it tells you which of the Buttons 1-3 does what, this will be important in a bit.

Scroll down to 'Controls' and press Enter.
This will open a window which looks like this:

Now, to use the pre-set mapping simply click the box in the upper-left corner and click okay. Your controller buttons 1-3 as well as your D-Pad or Left Analog stick should now respond as soon as you get back into the game. You might notice though that those controls are limited to jumping, shooting, restarting and moving. Pausing the game or entering the options menu is only possible via the keyboard if you do it this way.
#2 - Fully customized controls with JoyToKeyTo fully customize your controls, as you have already picked, JoyTokey is a good option. You'll need to know which button on your gamepad is labeled with which number though.
To find out which button on your gamepad is set to which number (At least on Windows 7, sorry I don't know how to do it on any other OS) follow these steps:Start Menu > Control Panel > Hardware and Sound > Devices and Printers
Right-click on your gamepad > Controller Options > Properties
Now you will see a window that looks like this (excuse the German text.)

Try pressing a few buttons on your gamepad now. The red circles with numbers should light up corresponding to the buttons you press. Memorize which buttons are which as you will have to assign them to different keys now.
Go back to the
Boshy options menu and set the controls back to
keyboard mode. As you do this this menu should pop up:

Simply press OK to exit it and now open up
JoyToKey.
In it, click
Create to create a new profile, and name it anything you like.
Here's where your button numbers come in, you'll have to assign the different keyboard keys used by Boshy to your gamepad. Here's a quick overview of which keys do what in the game:
Left Arrow Key | | Move Left |
Right Arrow Key | | Move Right |
Down Arrow Key | | Move Down (used in vehicle segments) |
Up Arrow Key | | Move Up (used in vehicle segments) |
Shift | | Jump |
Z | | Shoot |
R | | Restart |
Q | | Suicide |
Escape | | Open Menu / Cancel (in menus) |
Enter | | Confirm (in menus) |
F2 | | Restart Game |
F3 | | Character Select |
F5 | | Trophy Overview |
F8 | | Toggle FPS display |
Page Up | | Speed Up music |
Page Down | | Slow Down music |
Home | | Reset music pitch |
Decide which buttons you deem important, click on 'Bulk assignment wizard' and then simply input the keyboard key you want that button to act as. Stick1 is the left Analog Stick, Stick2 is the right one, POV is the D-Pad. The rest should be relatively self-explanatory.

And that should be everything. If you have any further questions don't hesitate to ask.