I am not well organized enough to use a lot of technology to do my research. All I use are books, a word-processing program, and the internet. Nevertheless, if you need to be better organized than I am, there are a lot of technological tools you can use.
What I basically do is put everything in the actual word document that I am working on. A bibliographical reference goes in the work cited. A paragraph from a primary or secondary source goes into the body of the text. I don't first collect data somewhere else and then write. I simply begin writing from the beginning. Where this doesn't work so well is when I've neglected to collect a complete reference and have to go back to check a book out a second time from the library.
Your most sophisticated piece of technology is your brain. Everything else is just a way of storing information in retrievable form.