I have recorded a Photoshop action that should help automate the process of converting caps with transparency.
It's fairly simple, and makes the process only take a handful of clicks per cap:
1) Open up the new cap template in Photoshop.
2) Open up the cap you want to convert. Make sure it is the foremost image, and the new template is behind it. Note that they are still separate images at this point.
3) Run the action. You will be prompted to choose the topside brim, main cap and underside brim colors. It will then save the modified image:
A few notes:
1) Photoshop seems rather persnickety about the order in which you open up the images. Opening up the cap and
then the new template seems to break the action, even if you make the cap the foreground image. So make sure the template is the first image you open.
2) This will overwrite your cap file without prompting. I strongly advise that you make backup copies of any caps you plan on modifying before applying this action.
3) The action was created using Photoshop CS2 in Windows, so your mileage may vary depending on OS and Photoshop version.