Launch Fugu by clicking its icon in the dock.
Enter your iPhone's IP Address into the Connect to: field. Set the Username to root. Then click the Connect button.
Note: If you don't know how to find your iPhone's IP Address you can follow this tutorial: How to Find the IP Address of Your iPhone
If prompted for a password please enter alpine or dottie or whatever else you might have set your password to. Then click the Authenticate button.
Click the Go To... button on the toolbar. Enter /System/Library/CoreServices/SpringBoard.app into the Go To field. Click to select Remotely. Then click the Go button.
Now scroll down the right pane and locate M68AP.plist. Drag this file from the right pane to the left pane to copy it to your computer.
Control+Click M68AP.plist in the left pane and select Open from the popup menu.
The Property List Editor will open M68AP.plist. Expand root, then displayOrder, then iconList. You will see a list from 0 to 12. This is the order for the first 13 icons (ie the default icons) on your SpringBoard. The icons are counted left to right, up to down, starting at zero.
Expand one of the numbers. You will notice a property called displayIdentifier. It is this value that sets what icon gets displayed in what spot.
The 13 default displayIdentifiers are:
Text - com.apple.MobileSMS
Calendar - com.apple.mobilecal
Photos - com.apple.mobileslideshow-Photos
Camera - com.apple.mobileslideshow-Camera
YouTube - com.apple.youtube
Stocks - com.apple.stocks
Maps - com.apple.Maps
Weather - com.apple.weather
Clock - com.apple.mobiletimer
Calculator - com.apple.calculator
Notes - com.apple.mobilenotes
Settings - com.apple.Preferences
iTunes - com.apple.MobileStore
You can expand each of the numbers and change its displayIdentifier to modify the order your SpringBoard icons are displayed.
Now this is fine for setting the order of the default icons but what if you have third party icons that you would like to order as well. (ie Installer, SSH etc). Well first we need to add another number to the iconList. Select number 12 then click the New Sibling button.
You will notice that 13 now appears under the iconList. Change its class to Dictionary.
Click the right arrow to the left of 13 so that it changes to a down arrow. Now click the New Child button. Name the property displayIdentifier and set is value to the displayIndentifier of the application you would like to appear in position 13.
If you do not know the displayIdentifier of your third party application you will have to go find it. I will show you how to do this for the Installer application. It is the same procedure for every other application.
Go back to Fugu. Click the Go To... button on the toolbar. In the window that appears select Remotely then enter /Applications into the entryfield. Now click the Go button.
You will now be displayed a folder list for all the applications on your iPhone. Double click to open the folder of the application you are looking for. In this case I will open the Installer.app folder.
Notice a file called Info.plist. Drag this file from the right pane to your local filesystem in the left pane.
Control+Click the file (Info.plist) in the left pane and select Open from the popup menu.
A new Property List Editor will open the contents of Info.plist. Expand root and take note of the CFBundleIdentifier value. This is the value we will use as our displayIdentifier for the application. In this example the value is com.apptapp.Installer.
Now back in the Property List Editor for M68AP.plist we can set the displayIdentifier string of icon 13 to com.apptapp.Installer.
Finally choose Save from the File menu then exit the Property List Editor.
Back in Fugu click the Go To... button on the toolbar. In the popup that appears make sure Remotely is selected then enter /System/Library/CoreServices/SpringBoard.app into the Go To: field. Now click the Go button.
Now drag the M68AP.plist file from the left pane to the right. When prompted whether to overwrite or not click the Overwrite button.
Hold down the Sleep/Wake button for three seconds. Once the Power slider appears drag it to the right to power down. Once the phone turns off click the Sleep/Wake button to power it back on.
You should now have Installer.app appear first after the default icons. ie installer will be in position 13 (14th icon), to the right of iTunes.