Swamp cooler purge pump

After much wailing and gnashing of teeth today, and an expensive lesson in just how much I don't know about swamp coolers, I replaced my ancient swamp cooler's bleed line with a purge pump. I've never seen one in action before.
Is it normal for the purge pump to run the pan completely empty, to the point of leaving both pumps running dry for a few minutes? It seems excessive to me. I figure I'd want to leave just enough water in the pan to keep the pad pump going.
I added a clamp to the purge line to restrict the water flow. Thinking about it now, that's probably a mistake. The correct move might be to elevate the purge pump, maybe 1/4" or so, just enough so that the pad pump doesn't run dry.
I know I'm nitpicking over details that probably don't matter. I just want to understand how this jury-rigged pile of rusty sheet metal is really supposed to work.
Thanks, -Scott
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Scott wrote:

Instructions for this model says it leaves "less than 1/2" of water"
http://www.kennspenns.com/coolerparts/powerclean-installation.html
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