If you are wondering how to set up some custom text tones manually, without using a cydia app or your cydia app just isn't working, we're going to go through some very easy steps.
** This tutorial is using Windows
** EDIT: Images coming shortly
First, We'll do SMS tones.
Step 1:
Make sure you have SSH enabled ( I'm sure you can find an SSH setup tutorial somewhere on these forums, or google. )
Step 2:
Now it's time to decide what sound you want to use for your custom tone. For this example, we'll use the classic mario coin sound.
Save this wav file to your desktop:
http://themushroomkingdom.net/sounds/wav/smb3_coin.wav
Step 3:
Once you've saved it to your desktop, open the wav file in iTunes.
Step 4:
To make this a little neater, in your itunes search bar, you can type in "smb3" so only your wav sound we are working with shows up. Now, in order for the sound to be recognized by our iPhone, we're going to have to change the sound format. This is accomplish by first going to:
Edit > Preferences > Import Settings

Once you are in Import Settings, in the Import Using Option, select: AIFF Encoder
Step 5:
Now that iTunes default encoder is AIFF, right click on your sound, and click "create AIFF version"
Step 6:
Once iTunes makes the new version, drag your new file to your desktop
** For this step, make sure that you have windows explorer set to show file extensions
The file on your desktop should read "smb3_coin.aif"
Since we're going to replace one of the original iPhone text tones, we are going to rename it.
Let's replace the shitty "glass" tone, which your iPhone knows it as sms-received3.caf
So, we rename it to just that, sms-received3.caf ( make sure you dont name it sms-received3.caf.aif as it wont read. The whole point of this is to change the extension as well )
Step 7
Now, it's time to replace the tone. Using your SSH client, ( I use winSCP ), open up your iphone and go to the follow folder:
/System/Library/Audio/UISounds
Drag and drop your new tone and Replace the old one that is in there.
Once you have done this, Respring or Restart your phone, and it should now make the Mario Sound.
Step 8: For WhatsApp Users
Since whatsapp actually uses its own sounds ( copies of the iphones ), we'll just use the same steps above.
The fix for this is simply going to your applications folder via SSH, Whatsapp.app, and replacing any of the .caf files that are there with your own following the steps in this tutorial.
I hope this was clear as it is my first tutorial, and someone requested it.
Cheers