You'll have to update the PHP and/or CSS for the gallery you are trying to change too. The properties.php file controls the image sizes that are created whenever you upload an image or update the watermark settings. If you are talking about the image size that is displayed when viewing a gallery, that will have to be updated as well to use whatever size you want. There are some other threads in this forum that have some details about this.
I'm not sure what you mean you can't have different size galleries? The properties.php file creates the various image sizes, then the galleries use those various sizes. The galleries we ship with for instance, use different thumbnail images. Those image sizes are specified in the properties.php file.
You can make your own gallery by copying one of the folders in the galleries directory, then modify the files how you need. Check out the how to on the support page: powergallery/. If you have any more specific questions about changing something, let me know.