Here is the way to change only the file folder colors in IconPackager. You may think that it is a long roundabout way, but it actually doesn't take that long and it is kinda fun and it's easy to do
Step 1 : The first thing we'll need to do is build a new, but only partial, IconPackage, but in this package we are only going to include the File folders that we want to change the color. The other default icons in the builder we will not change since we won't be using them anyway and will be deleting them later.
Step 2: In the IconPackager User Interface select the Icons & Cursors Tab. Navigate to the bottom left and select "Package Builder"
Step 3: Now that you are in the Builder, drag and drop ONLY the file folder icons that you want to change the color, all the other default icons in the builder you can ignore. We won't be using them anyway and will be deleted when we complete the color change.
Step 4: When you have completed step 3 and have all the icons added in the builder that will get a color change, navigate to the top of the Builder window and click on "save as " button. A new window will open prompting you to choose a name for the new package. Just make up something, it's not important because it's not really going to be a package when we complete the color change, name it something like "Color Me Folder" or something like that. Be sure to save the new package you have created to the IconPackager Folder at -- C:\Users\Public\Public Documents\Stardock\IconPackager
Step 5: When you have saved your new package folder to the proper loacation in IconPackager, open the IconPackager Program and you should see your newly created package in the previews. Click once on your new package for it to be displayed in the preview window , then select "Change Icon Package Color" from the left menu options and proceed to adjusting the colors to your liking.
Step 6 : When the colors are adjusted to your liking ,then go ahead and apply the new package to your desktop. Don't panic here ! it's just temporary so that we can save it with our new colors.
Step 7 : Now that it is applied , select the "icons & Cursors" tab at the top of the program, then select "save icon package" > "save icon package as" ....here , if you want to preserve what you just created for re-coloring again in the future then give this precolored package a new name, like say....."Color Me Folder v2". It doesn't matter where you save this folder because we are going to be stripping it down anyway. To make it easy, just save it to your desktop.
Step 8: Now that we have our folders re-colored, we need to put them back into their original IconPackage folder, NOT the new one you created, but the ORIGINAL package that you didn't want all the icons re-colored. But first you want to make sure you create a backup or copy of the origianl IconPackager in the event that you want to change things back to the way they were originally.
Step 9: This part is extremely important and you must follow the direction here EXACTLY so that all the icons will display correctly. We will simply be doing a copy & paste operation here by copying the new colored folders and pasting them in place of the original folders. Therefore, it is very important that you" rename" the new colored folder to the EXACT name of the folder you are replacing.....an example would be , if the original folder was named "Metal Storm Icon 26.ico" then the new colored folder that is replacing it must also be named "Metal Storm Icon 26.ico" When you attemp to paste , a warning window should pop up telling you that there is already an icon with that name and will ask if you want to replace it, you will of course click "yes"
Step 10 : You should now have all of your new recolored folders in place of the originals. Now you can open up the IconPackager Main program and apply this newly customized package. You can also delete the temporary package that you created in IconPackager to do the recoloring, plus the temporary one that you saved to your desktop.