They are to be run with a stack.
The FMS is fuel only, it does not do timing at all.
I'm running a FMS with a 1 off CaTCHER (old school Smarty) that does not have timing. I actually, at one time, had a Blue Chip, CaTCHER, Edge EZ stack.. I notice a little difference when I got rid of the timing, but you cannot compete with the clutch eating torque off the line.
The FMS is the most adjustable box on the planet. It does NOT do the de-fuel shutter that the TST is famous for. If funds are not an issue, this is the only box I would ever run.