I believe I can answer this one if I understood your question correctly. I believe you want to perform an autonomous PSS analysis followed by a pnoise analysis. There should be no independent periodic sources in your schematic. However, you may have non-zero DC and perhaps AC sources. I believe the "input source" entry in the pnoise form defines your input point for noise figure analysis. Since you are interested in phase noise, not noise figure, you are free to chose any independent dc or ac source you like. (By ac I mean small signal frequency domain source, one that does nothing in a tranisent simulation.) The source you chose makes no difference in your phase noise analysis.