iTunes only supports a "Media Folder" in a single location, although there are some workarounds to store pieces elsewhere.
That said, however, you can tell iTunes to import music from whatever location you decide to put it in and leave it in that location simply by going into the iTunes Preferences and UNselecting the option to "Copy files to iTunes Media Folder" on the "Advanced" tab. With this option off, any music you import into iTunes will be left in its original location and referenced from there. Just be sure to put the files in their permanent location right off, as iTunes will lose track of the files if you start moving them around after you've imported them.