The realtime PCR community is finally cracking down on poorly designed experiments. If you want to be able to publish your data there is now a set of guidelines to follow. Bustin et al published the MIQE guidelines, and here is a practical guide to follow when designing your experiment.
Where to begin? Assuming you have extracted and tested your RNA, performed RT-PCR to generate cDNA, here is an outline of how to setup your first qPCR experiment.
No matter which instrument you use or which chemistry you prefer. The number one cause of variability in CT values is degraded RNA. You will no longer be able to publish results without being asked the question "How did you verify the quality of your RNA?"