Working With Linked Resources
From FDT Documentation
Some developers like to have source code, either via a SWC or .AS files, saved on their workstation but not in the same location as their project. The solution for this is to use FDT's 'Linked Resource' feature.
Begin by right clicking on your project and selecting 'Properties'.
FDT will then open up your project properties panel.
Once here, if you have already created bookmarks for resources, you can choose them. If not you can click 'Add' to create more resource bookmarks.