I'd like to do whole cell patch clamp recording in co-localized mouse medial frontal cortex neurons projected from ventral hippocampus and basolateral amygdala using retrograde dye injection.
We use fluorescent retro-tracers, read beads and green beads, for experiments similar to what you described. The reason we chose these retrobeads was based on this article (http://www.ncbi.nlm.nih.gov/pubmed/18428673), in which the authors compared the characteristics of some commonly used retro tracers. I'd suggest you take a look at the article, it'll guide you to find the tracers that suit your experiments.