To use Tooliphone, you just need to point your iPhone’s Safari browser to Tooliphone’s website. Here, you’re given two options: iEmpty, which makes blank app icons (good for creating a custom layout), or iCustom, which allows you to create app icons. From there, you pick the app you want to customise, point Tooliphone to an icon (online or on your device), and then Tooliphone creates a shortcut with the icon of your choosing to the app.
It’s a roundabout way to change the icons that takes a bit of work, but if you don’t feel like jailbreaking, it’s an option that works. Alternatively, you can go into your device and do it manually.