deciding if 2 pops are the same, and if negative.

Hello!
I wanted to ask what methods do you use to determine if two populations 
expression is the same for a given marker. let's assume i have cells "x" 
before and after treatment, stained for DR (the same Ab used in saturating 
concentrations). Given that we acquired 1000's of cells almost any 
difference is statistically significant, and KS stats are very rigorous - 
too rigorous it seems to me. Now, we have cellquest pro, don;t have flowjo 
and FCS express which i understand have better statistical tools. How would 
you decide the cells express DR in the same extent (let's assume all else is 
similar: unstained profile, isotype control binding, etc)?  if they are 
different by 5%? if we were to take the 2 (or 3!) SD criterion we would be 
doing the opposite of KS - even very different expressions would be "the 
same", specially if the distribution of DR is not too uniform. The same 
affects for deciding that a certain marker is not expressed. How far from 
the isotype control would you say negative and not "very low expression"? I 
am purposefully leaving out the sensitivity and Q&B questions, since getting 
too technical would make things too complicated for day to day work. The FC 
i have is what i have! What i do have is CV determinations using fluorescent 
beads. I am referring to the "typical" scenario where there is the isotype 
distribution and a very close but not matching "stained" distribution. Of 
course I could apply the same criterion for stained vs isotype as i do for 2 
stained populations, but i wanted to know if there are special or specific 
matters regarding the "no expression" determination in contrast to 
"different expression".

Thanks a lot!

Uriel.