Yes, run the trans through the gears, pausing for a few moments at each. Do this two or three times during the flush so can circulate cleaner fluid into the nether regions.

BTW Unless you're quite careful about measuring fluid drained, flushed, refilled, it's easy to overfill when you're done. Best to stop a little early on the final fill and take a measure. It's roughly one pint between max-min markings. If you do overfill then simply disconnect the return line again and run a little more out using the trans pump. The FAQ suggests opening the pan drain screw to do this, but in my opinion that's way too messy, you have to jack the car up again (it's easier to do the flush operation without the car raised), it's too easy to drain too much out, plus I don't like having a panic attack if the threads don't easily catch when I'm done. And speaking of mess, if you've ever wondered why people don't like to drop the trans pan to do a full drain and cleaning just remember that there's a lot of fluid sitting up in the gears and passageways that can take days to stop dripping. If you ever have to replace a kickdown cable you'll know what I'm talking about.
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Dave -940's, prev 740/240/140/120 You'd think I'd have learned by now