A skimmer is intended to pull the surface dust, leaves, dead algae etc into it. It will also draw any floating plants like hyacinth and duck weed. While lily leaves may not go into the skimmer itself any stuff floating on the top of the pond will jam up against the lily leaves so the skimmer is no longer skimming. I've placed my lilies in my pond so that the current from the waterfall to the skimmer is not impeded by lily pads. I'm not sure if lily leaves in the way would cause a problem with the skimmer clogging--if my pond is too full the pump still draws water from the skimmer but draws no surface leaves, litter etc. I'm more concerned that the lily may impede the flow (like a dam) and the skimmer will not have enough water in it causing problems for my pump and also restrict the circulation of the pond.

I haven't had any trouble with that problem. My skimmer is on one end of the pond, with the waterfall on the opposite side. I have my lily planted in a large but shallow pot, and it is setting on the bottom of the pond closest to the skimmer because the water is very still there.

Here is a picture to give you an idea.

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OK, I see, but Jalal made a good point about the pads creating a damming effect and restricting the water flow into the skimmer. No problems there? I guess I could try to keep them more toward the sides.

I haven't had any problems as far as a damming effect. Water will just flow through, around and under the leaves.

Worst case scenario, you have to rake a few dead leaves and such from between the lily leaves towards the skimmer.