S phase?/WinMDI

Hello!

We are using BD FACS Calibur for the cell cycle analysis of different  
human tumor cell lines. Subsequent to the analysis, we use WinMDI for the
data analysis, but have a major problem in determining the exact 
position of the S phase, i.e. we are having doubts on where to position 
start/end marker for the S and G2 phase. We heard that some labs overlap 
the phase markers, but we are not sure if this is the right way to do 
this, as this poses the question if the sum of the percentages of the 
cells in each phase would then exceed 100 %. Is there any other flow 
cytometry software better than WinMDI that would allow us to precisely
recognize the position of the S phase or which automatically marks the 
phases?
If anyone has some good reference on the subject presented above, we 
would greatly appreciate to send us.
Thank you.
Looking forward to your suggestions :-)