In the Hue Map Dialog Box adjust the hue of the yellow color and the saturation and lightness levels until you get the color you want.
Click the Save button.
Click the Close button.
Close the flag file you opened.
Go to File > Batch > Process
On the Look in Menu choose one of the folders that contain original flags.
Check Run Script in Silent Mode. Browse and find the Flag Color Script.
Set Save Mode to Copy if it isn't already.
Set the folder under save options to the corresponding new folder you created in step one. The dialog looks like this:
Click Select All to start the batch process.
When it is finished, click OK.
Repeat the Batch Process for each folder. It remembers your settings so all you need to do is change the folders.
If you increased the lightness, you need to change the background back to black on all your new flags. This is because only an exact black color shows up as transparent in the game. To do this, run another batch process on each of the new folders you created. This time change the Script to Background Color Change and change the Save Mode to Overwrite.
To create a new flag stick just open up the original, play with the hue map and other settings, and save it in the new pin folder you created in step 1.
Now take your folders and install them in the game like any other flags. See the flag installation instructions for more details on how to do this.