There are a number of rental websites you can utilize in your search:
This map will show you the various neighborhoods of Fremont:
As far as finding a "good" middle/elementary school area home to rent, I would recommend you use http://www.schoolandhousing.com as they have the most user-friendly website I have come across. Besides the fact that they include private schools, what is really nice about their website is that it also shows performance information for the elementary/middle/high schools a specific property address is assigned to.
You should always call the Fremont Unified School District office to confirm the attendance schools before entering into a rental agreement. http://www.fremont.k12.ca.us/Page/274
You can start with looking at the website, craigslist.org for 'homes for rent' (see link below)
Fremont has approx. 25 elem. (K-6) school and most all are great. And five Jr. High & five High Schools, also very good. Pricing will be higher in the Mission area, however there are several options.
Real Estate / Property Management
The rental market is a bit tight right now. The good homes go VERY quickly (which can make it difficult if looking for a rental remotely). But to get you started, I have a post a link to some search resources. My best guestimate, is that a 3bed/2bath+ home in the Mission Valley (mission san jose area of Fremont), you're probably looking at about $3k/mo minimum.