I searched for a long time on stackoverflow using every keyword I could think of to solve this. I am programming for iphone and I have a lite and paid version of my app. I
For each resource (or folder of resources) you want to direct to a specific target, you can click on the resource and inspect it (either via right-clicking and selecting Get Info or by clicking on the Inspect toolbar option). Within that info dialog will be a tab called Targets, where you can check the targets you want the resource (or even source code file) to be incorporated into, and uncheck the ones you don't.
Alternatively, I believe you can navigate to the target itself in Xcode, click on the triangle next to its name to expand the list of build phases, expand the Copy Bundle Resources build phase, and manually delete from the list there any resources you don't wish to have copied over into that target.