Dear Smith,

With the little knowledge of working on FACS, I think you can try following, -

If all the sample are of same origin/cell type then try labeling a few samples initially in order to get an idea where these cells (dead) lie on your plots. Select the live cell population carefully and store the files. Compare the same sample without adding the dead cells marker and if you can differentiate live cells from dead cells without any confusion.

If using PI for differentiating dead vs live cells, then acquire the sample before and after adding PI. This might help as well .

OR

If you have say 1 control and 3 treatment groups then try labeling 1-2 representative samples to get idea to differentiate dead and live cells.

All the best.

Each marker should be analyzed under living cells, so you need to label all samples.