Biological membranes are known for their complex nature and formation of domains is crucial for proper execution of multiple cellular processes. Such domains, mostly due to their nanoscale character, are rarely studied since implementation of techniques for their quantitative investigation is difficult. In this article we introduce spot-variation z-scan FCS implemented for the first time for artificial lipid vesicles of defined lipid composition. We used this approach to investigate behaviour of different species of ceramide-1-phosphate within membranes. We were able to provide quantitative description of lipid domains generated by ceramide-1-phosphate in nano and microscale. Aligning these results with in silico studies helped us to validate the approach and draw conclusions on complex behaviour of signalling lipids within biological membranes.