Under 100 dollar per night is going to be pretty hard to do in San Diego any time of the year. In August it's going to be downright impossible.
That said, I would try Mission Valley hotels first; the Days Inn & Suites in Mission Valley is a good bet that I've used repeatedly. Not sure you can get it under 100 bucks, but it'll be pretty close. Spend some time on Expedia or Hotels.com and see what you can find. The Red Lion Hanalei is bigger and plusher and I've always been happy there, but you aren't going to find it for under 100 bucks.
If Mission Valley doesn't work for you, just try and stay in the areas north of downtown proper. When you go south of downtown you enter the grittier part of town around the naval yards and the older working class suburbs. It's not anything to write home about, and there is very little to do around any of the motels in that part of town. When you get within a few miles of the Mexican border you are entering some rather unsafe and ugly neighborhoods. Steer clear of the border area entirely, and don't even think of going across the border to Tijuana. Tijuana is no longer safe for anyone and gun fights and kidnappings and horrible crime run rampant in the broad daylight there. No one goes to Tijuana anymore, ever.
Also realize if you go below 100 bucks per night, you are really gambling on the quality and safety of the motel or motor inn. If you find something for under 100 bucks per night, do plenty of research on the place on Trip Advisor or Expedia customer feedback.
You might try heading inland a bit on the I-15 corridor instead of the I-5 coastal corridor. The northern inland suburbs are pretty nice, and its much cheaper than the coastal communities. You will have to do some driving in the 15 to 30 minute range to reach the tourist spots like the Zoo, Sea World, La Jolla, beaches, etc. though.
