I'll post up a quick one on here, in case someone else wants to see it. Just FYI, all this is Mac based, so the steps may be the same for Windows but the programs may differ. You'll have to find a suitable replacement.
1) Download OpenSSH from Cydia. This program will install a client on your phone that can communicate with your computer wirelessly or wired, allowing you to access the basic file structure of the phone.If you ever used an FTP client, that's what this is.
2) Download a program called Cyberduck for Mac onto your PC. Cyberduck – FTP, SFTP, WebDAV, Cloud Files, Google Docs & Amazon S3 Browser for Mac & Windows.
3) Fire up Cyberduck, and click on "Open a Connection". What you are doing here is telling your PC to connect to your iPhone. You will follow the instructions here: How to SSH into the iPhone from Mac with Cyberduck?
You will see it connect to your phone if you did it right, and it will reveal a couple folders in the root filesystem of your phone.
4) Navigate through this filesystem by going to the dropdown menu on Cyberduck that says "private/var/root". Select the top file folder, which is the main menu of the phone. You should see folders like, system, applications, bin, boot, etc . on the list. Go to "LIBRARY", then to "THEMES". All of the main folders for your uploaded themes should be showing.
5) By now, you should have an icon saved on your PC (or customized one of your own) that should be in .PNG format and 60x60 pixels in size. You can make them any size you want, but 60x60 is ideal and as close to "stock"as you can get. On Cyberduck, find the folder name of the theme you wish to modify the icons for. You'll see a folder named "ICONS" within that folder. These are the special icons that replace the standard ones. There may also be .png files in the main theme folder, and they serve the same purpose.
6) In Cyberduck, you can delete and replace the icons you want to replace. Just make sure you use the EXACT filename for the replacement icons- they are case sensitive too! If you screw up and they don't work, no worries...just delete and re-install the theme and start again. It's trial and error sometimes, but this is the best way to learn the basics of altering your filesystem and also creating custom themes.
I tried to write this for the layperson without too much jargon. I hope it helps. If anyone else can chime in with a step I forgot, please do so. And if I screwed something up, let me know too! LOL