Some times a will see a Qur'an that has Allah's name written in red along with any one of Allah's other names or pronoun refrences to Allah (huwa, etc.). I was wondering if there was any reason they do this, whether or not it is an innovation, or if there are some special tajweed rules or sunnah acts that one should observe when reciting Allah's name from the Qur'an.
There is no basis for doing that. All the words of Allaah should be printed in the same colour. This is a kind of innovation that has been introduced into the Mus-hafs.