Handling controller inputs on multiple platforms

I was just wondering (really almost academically) how it's best to deal with different controller inputs on different versions of your games. For a VERY basic example. I am currently testing a project of mine on my Mac and my PC where I use different controllers with different mappings in the Input Manager. This isn't currently a giant issue due to the fact that there are alternate fields available and none of my current fields overlap. Is there a way to programmatically assign the input manager or is the general practice to make totally seperate projects for different platforms to account for any number of various platform specific changes that are being made?