Here's the bible for gravity-fed water systems:
NeatWork Software
You'll need NeatWork for your aqueduct design. There is other design software out there, but I found NeatWork to be very good.
- Agua Para La Vida - NGO Focused on rural water systems in Central America
- Waterlines - NGO Focused on rural water systems
Another Peace Corps Blog
Here's the blog I kept during my Peace Corps service. It won't necessary help with the construction of a water system, but gets at some of the social issues one may encounter working with rural communities in developing countries.