The origin is from Spain. Check this website:
http://www.houseofnames.com/xq/asp.fc/qx/santisteban-family-crest.htm
I think the i in the surname is similar in usage to the Spanish word "twenty-five", viente y cinco , which could also be spelled "veinticinco"
where the e & y are changed into an i when it's a combination form: So, Santisteban = Sant(o)[It is from the Latin word for Saint]? + Esteban, meaning "Saint Steven" in Spanish. But in Europe, they spell "Steven" as Stephen. So, it should be "Saint Stephen".