New Pool Owner Building a New Pool

Do you know if we can choose which side of the cover box contains the motor (that extends 2-3 feet beyond the edge of the pool)?
Yes, the motor can go on either side. You might want to just give them a call and talk through different options. Their office is in Lindon. I actually went in one day to look at cover colors, and they have one set up to talk through different options.

For my own pool, I didn't add an overflow. We don't get enough rain usually to make it an issue, but I have two drains in the cover box that water will flow into first. I don't know if that was a bad idea or not, but it's what I'm doing.
 
You won't need an overflow with an autocover that has a pit. The lowered wall of the cover end serves as an overflow, for better or worse. What I mean by that is you will lose more water than you would otherwise when people jump in. When the water is high you'll lose if faster than if you keep it just a little lower.

There's frankly not a great solution to autocover placement when you plan to have the whole deep end be a rock wall. Most of which have been discussed above. The corner rock wall does solve the problem - in that it cantilevers over the end of the cover - and may not look out of place in your siting of the pool. If you place the pit in the shallow end (not ideal but if you have a shelf you can try a pool rule that primary entrance is from the sides of the shelf - you can still use it to walk on but it's not meant to be jumped on, etc.), you can go with a cover type that some offer which utilizes a fully retractable cover. In reality, it's that the pit cover extends farther over the cover than normal. So instead of 12' coping on that end, you would have up to 24"coping. Here's a link. It seems most cover brands don't offer this, but CoverPools does. Brackets that extend 24" out over the pool make me a bit nervous from an engineering perspective, regarding the live load on then. They handle the static load fine but put a 300 lb'er on them and have them at the edge of the stone, and they hop a bit - eesh. That's a lot of force - but they do make them so they are probably fine - though not everything sold is great for its intended use.

Lids and Benches - Cover-Pools
 
For what it's worth, I'm getting the 13" vanishing lid bracket that @bmoreswim linked to. Part of my cover will remain exposed though, similar to the photo I posted. I would also be worried about 24" brackets, but I'd just call and ask them about it.
 
We have ~110 ft run from the pumps to the pool, and ~16" elevation on the pump, with three 90's in the line. Should I have any concerns about stress on the system? We could eliminate one of the 90's by changing to 45's, but that would cause a re-trenching hassle to run at a 45-degree angle. Any thoughts??
 
We have ~110 ft run from the pumps to the pool, and ~16" elevation on the pump, with three 90's in the line. Should I have any concerns about stress on the system?

No.

What size pipes for the 110ft run? Use 2 1/2" - 3" pipes and all will be good.
 
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