Most times you might be facing problems like "Singature error". I will give you some instructions on updating Superuser. Here's what you will do:
1. Open Google Play Store and install the "System Apps Installer'' application. It is free and it is compartible with Galaxy Y.
2. Open it and grant superuser permissions to the app.
3. At first, you will see a File Manager. Browse through your sdcard and find the new Superuser app version you have downloaded and you want to install.
4. For example I will install Superuser 3.1.3 . Now find the apk and click it.
5. It will know say "This app already exists. żDo you want to overwrite it?
6. Press yes and wait to install.
7. When it's done it will say "ĦApp installed correctly!
8. Open the new Superuser and update it's binary.
9. You're ready to go.
From now on, if Superuser has ever an update released, you will be able to update it succesfully from the Google Play Store.
Personally tested and working on Evo-x4.2
Get the APKs needed in the attachment below.
P.S. You can use that method too for other apps that you can't update.