I assume from your mentioning having an air trap, you want to mount your eheim with the inlet facing up into the bottom of the airtrap and the outlet pointing out horizontally across the case.
Nod if this is so?!
If that is the case, you shouldn't have any problems with the pump. However, you might want to take measures to prevent a "whirlpool" from allowing air to get into the pump.
8-ball
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