There are many books, publications, publication collections, and other resources available to help you learn about the history of fly research, basic information about fly development and physiology, and how to perform genetic and other assays using the fly. Here are just a few places to start.

The "Genetics on the Fly" primer by Hales et al. (2015) provides an excellent distillation of background information relevant to Drosophila research.
The "How to design a genetic mating scheme" training package from Roote and Prokop (2013) provides information about how to set up and 'score' fly crosses, such as using visible markers.
GSA Genetics journals' FlyBook chapter series provides expert background information on many areas of Drosophila research.
The Interactive Fly provides background information about Drosophila development.
The Manchester Fly Facility provides background information and links to additional resources for information about flies and fly research.
The FlyBase Resources wiki page lists information, protocol, reagent, and other resources relevant to Drosophila research.
FlyBase also maintains a FlyBase "new to flies" wiki page with links to additional resources.
The "Culture of Drosophila: the laboratory setup" article by Ashburner and Roote (2007) discusses basic fly lab needs like incubators and fly food.