I want to take advantage of the fluid grid layout guides with preset number of columns but I want to use the twitter bootstrap files instead of the integrated DW bootstrap files. Can this be done? Seems using "New fluid grid layout" forces us to use DW's files and if I just start a new blank page and bring in the twitter bootstrap files, the fluid grid layout guides don't do anything.
That's right. FluidGrid Layout guides only display in a FluidGrid Layout.
You may want to invest some time in researching some of the online and offline grid tools. For example, Pinegrow does what you want and works with bootstrap, Foundation (and any other framework potentially).