First you need to fill out your FAFSA form at FAFSA.org. The deadline to fill this out by FAFSA is in the beginning of each year. Also, you usually have to fill out a separate financial aid form for your school. The deadline for this is usually different, so I would check with each individual school.
However, if you cannot make it by the deadline, FAFSA will still accept it, as will most schools, so no need to worry. If you don't fill out the forms by the required date though, then you might qualify for a smaller amount of loans, scholarships and grants because after that date, you basically qualify for what and any funds that are left. I have filled out my FAFSA and financial aids late before, and i noticed no difference in my scholarship/financial aid package though.
I received all of my scholarships directly through the school I attended. I received a scholarship package of $16,000 a year, plus some financial aid.
You can also receive scholarships through websites and private organizations. I have tried to apply for scholarships through private organizations, but I felt that for most scholarships, a lot of work was needed. They might want a very long paper, an invention, some sort of research project and so on. I am NOT saying these are a waste though. I have met many people who have received these private scholarships.
For masters programs, the schools in my area do not offer ANY scholarships or financial aid (besides loans) for any of their MBA programs. This is very upsetting because I got into all of the schools I applied to, and I didn't know that masters programs only offer loans. This made the price of going to graduate school much higher than for my undergraduate degrees.
Some websites that I would check out are:
Have you had any luck with receiving scholarships outside of the ones that your school gave you?