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I think maybe you should point them upwards a bit more, but the placement seems fine. It will change of course after you get rock in there as it will change the dynamics of the water flow.
One more question...I have the two pumps on a "wavemaker" timer, they basically just alternate every 15 minutes. But it really doesn't seem like there is much water movement with only one going at a time, and there definitely aren't any waves. Would it be better to just have them both running continuously?
i think it's up to you. If you think the flow is lacking then by all means run them both. I have mine set on a wavemaker and they alternate every like 5 seconds so I don't loose too much flow. Can you set the timer so it is closer together?