As far as I know, there's no template for counters. It's just open an existent counter and edit it as you will. Then save it at 8bit. If you have Photoshop it might work fine ingame.How do you create the counters? I know that there is the EFM for the shields and the flags, but is there also a template for the counters?
If you didn't edited it in Photoshop, but other program, you may have to convert the new counter to the correct color scale that the game uses to have your new counter working ingame. There's a small utility (that you can find in my blog, in Downloads section) that do the job.