Yes, the lower hose ... at least this is so on my '99.
Do not worry with "reverse flushing" .... only when the fluid is very still will anything drop out (such as in a pan)... nothing will drop out in the coolers, the fluid flow is much too high there.
It is not good to run the tranny empty of fluid ... that being said, it is likely you have done little or no harm. I like to use a helper (on the ignition key) for this process. I would just proceed if I were you.