Make use of Excel or another spreadsheet program for Gantt Charts, project time lines.
Make use of Visio for flow charting... You could also use MS Project for some other tid bits. If you are using a linux box, look into the Open Office package to find a spreadsheet, word processor, flow charting type of feature. Document it from start to finish. Polyphemus' response was correct, in that I would suggest starting with pen and paper... brainstorm on ideas of what you want to implement, weigh pros and cons and such. Going straight to code on any complex project is imminent doom
