(My guide on general Isaac tips and tricks can be found here)

Firstly, download Joy2Key here[joytokey.net] and extract it to wherever you like

Go into the extracted folder and pin the .exe to your taskbar and open it, it will look like this:







Rename Profile 1 'The Binding of Isaac'









Click on 'Options' and hopefully your gamepad has been detected. At the bottom set the analog stick thresholds to around 50% - if you aren't comfortable with their sensitivity ingame, you can change this to whatever suits you. I find 50% to be a nice comfortable setting.








Now go to 'Joystick 1' to set up the gamepad buttons:


You can now set the buttons to whatever you like. Moving/pressing the buttons on your controller will highlight which one it is on Joy2Key in yellow.











My setup is:


Setup:
Left analog stick moves Isaac
Right analog stick shoots tears
Active Items (Spacebar) are used by pressing A.
Bombs (Shift/E) are used by pressing LB
Pills/Cards (Q) are used by pressing RB
The menu (Escape) is brought up by pressing start






That's it! Enjoy Isaac on your controller! Remember to open Joy2Key each time before you play Isaac and close it when you're finished!