what exactly do you need the protocol for? Do you want to see the cells only in the FSC/SSC, do you want to do stainings - if so, which ones?, do you want to detect C. Glabrata, only specifically, etc.?
i did not understand the answer with the expressed epidopes and therefore i do not know what your read out should be. I can only give a general answer now.
If you only need FSC/SSC - have you already tried to FACS the cells? What do you see?
I mean, basically you only need to have enough cells in your sample to do the baseline settings. I.e. set FSC/SSC settings (if necessary reduce the threshold, because the cells are relatively small), so that you can see the population well.