With method 1 you may get both the fibroblast and epithelial cell adhering to the plate, with the SCC9's growing in tight colonies surrounded by the fibroblasts.  With method 2, you might get the epithelial cells actually growing on top of the fibroblasts, and not touching the plastic at all.  Clearly different conditions for the epithelial cells.  Choice depends on what culture conditions you are trying to establish.You might consider some  preliminary cultures to identify which approach is a better model for you.  If the cells cannot be distinguished from each other by bright field or phase, consider using keratin and/or vimentin antibodies.

Thanks dr. Bruce,

But do you mean by "clearly different conditions for the epithelial cells" in method 2, that the expression of certain genes might be affected??

If my aim is to examine the change in fibroblasts when they become co-cultured with SCC9 cells; in this situation... do you think method 2 wouldn't be the correct choice??

Thanks again

#2 is closer to normal orientation of the cells, fibroblasts below epithelium, although fibroblasts on plastic is not very physiological.  You might want to consider putting the fibroblasts on or in type I/III collagen. 

Depending on the proliferation rate of the fibroblasts, the amount of cell-cell contact between the fibroblasts (or time in culture; or seeding density) may influence the RNA profile of the fibroblasts at the end of the culture.  Be sure to run parallel fibroblast-only cultures as controls.

Thanks a lot Dr