It depends on what images you're talking about - the framing and gradient images for IE (such as for button corners, backgrounds, etc.) should be automatically generated by the Sencha Cmd slicer in the correct colors.
If you're talking about the other images, though, like grid header menu arrows, date field triggers, panel tools, etc. - these are not automatically managed by the framework. If you want to modify their appearance, you'll have to use an image manipulation program of your choice to do it manually, and then place the updated versions in the resources/images folder of your custom theme. It's a bit of a pain, but I can't see how Sencha Cmd could feasibly automate these kinds of changes - and it's still far, far easier than all the tedium that theming required in the days before Sencha Cmd existed.