As far as toe punching, it is really punching a hole in the webbing between the toes. They make little tools that do that. It is very permanent when done properly, but does not necessarily replace leg bands to identify individual birds.
If you didn't want to do toe punches you could use the temporary zip ties until they were old enough to put a regular band on. I like the one that are little plastic coils, they come in many sizes and colors.