well, the first questions should be:
(1) if we're in CYCLE when the E-Stop is pressed, do we want to "return" to CYCLE when the E-Stop condition is later cleared (and pick up where we left off)? ... or do we want to "start over" from the very beginning? ...
(2) if we're in WASTE when the E-Stop is pressed, do we want to "return" to WASTE when the E-Stop condition is later cleared (and pick up where we left off)? ... or do we want to "start over" from the very beginning? ...
(3) if we're in FLUSH when the E-Stop is pressed, do we want to "return" to FLUSH when the E-Stop condition is later cleared (and pick up where we left off)? ... or do we want to "start over" from the very beginning? ...
you'll have to nail down those answers before you can go much further ...
suggestion: if you haven't already done so, take a look in the SAMPLES folder that should have been installed with your RSLogix5000 software (do a File Open, etc.) ... there should be a couple of SFC examples in there – and the basic idea of jumping "out of" – and then back "in to" - the chart is covered ... that might be a good place to start ...