My solar is plumbed before my gas heater, and Allen explains why that's right.
I can barely hear my pump running through an exterior wall at one end of my house. I cannot hear "the vibrations/noise" of water running through my solar panels. I can hear the system at startup, purging air out of the panels. I couldn't say offhand if I'm hearing the air bubbling through the pad plumbing, or the air bubbling out into the pool, or the air through the panels, or what. Probably some of each? It lasts for less than a minute. And I hear all that because the pool, pad and panels are closest to my master bedroom, where I am most often when my heater first fires up. I doubt I would hear any of that from elsewhere in the house. But it's never woken me. Frankly, when I'm awake and still at that end of the house, it's fine knowing when the panels are first engaged. For reference, I have stucco walls and a concrete tile roof.
Way more important than any sound dampening, is the load of two sets of panels on the roof, and how they are connected, and how they move. Usually roofs are overbuilt to support weight, so a second set of panels might be OK, but weight is weight and less is better. But there are other forces at work beside gravity. Your array should be engineered to withstand wind loads, too, including how it is connected to your roof. How will two sets of panels affect wind load, and if the new panels are properly engineered for that, how will them laying on another set of panels affect their resistance to wind load? How will the second set affect the wind load characteristics of the first set, and vice versa. And even if the second set is properly attached to the second, was the first set ever properly attached? Or properly installed?
All of which is to say, remove the first set. Just sounds like the guy is being lazy, and unless he discussed the other issues and forces at work, he's just making stuff up. It could actually be a red flag. Lots of installers out there, not all of them know what they're doing. Can you get other estimates? Talk to other installers? See what they say about laying one set on another! In my area, I can't even lay a second set of asphalt roof tiles on the previous set. We used to be able to layer 'em three high!
And way more important than all of that, is the attachment. It's the attachments and penetrations that really matter. How strong are they? Will they support the loads (weight and wind)? Will they be water-tight for the next 20 years? Will the attachments allow expansion and contraction of the panels? Because they move around during the day and night. It's why I chose Heliocol panels. They have a great mounting system, which handles weight, wind, expansion and contraction in a simple and elegant way. My attachments don't even penetrate my roof's underlayment, so they cannot cause a roof leak. A suppose a hurricane could rip them off, but they've withstood ~30MPH winds so far. Works for me. The penetrations present the biggest liability risk to the installer. If he gets them wrong, not only will he be back to fix them, but he'll be liable for any water damage a leak would cause (unless he presents you with a contract that negates that, which you should be aware of). It could be that your installer is looking for an out. If you authorize the new set to attach to the first, then the installer could claim foul if your roof starts leaking. He could claim he didn't do the penetrations, and so he's not liable for them. And you'd be giving him permission to assert that!
You should have a conversation with him about all this. Does he offer a warranty? What does it cover? Will it cover the new penetrations, and just as importantly, will it cover the previous penetrations? Will that old set of penetrations be used? Left as is? Removed? Etc.
Your panels will have an optimal flow rate to generate the most heat for the least pump energy. That probably won't be your low speed, though you might get sufficient heating at low speed.
@mas985 knows more about that than I do. I have a variable speed pump, and my controller can ramp it up and down for optimal flow, heating and efficiency. If a variable speed pump is in your future, now's the time. You would, of course, make sure the new pump is compatible with your controller. Given your electric bill issues, a variable pump could ROI pretty quickly.
I installed a FlowVis flow meter to fine-tune my flow rate through my panels. The rate is the exact spec the manufacturer recommends. The FlowVis doubles as a check valve, so if your installation requires a new check, consider a FlowVis, especially if you decide to go VS pump. You don't need a FlowVis to get your system going, there are other less accurate ways to get in the ballpark of optimal flow, but I like knowing I have my system perfectly tuned.
If PV solar is a possibility (I have both), then consider its future placement. I put my pool panels in a slightly less optimal location on my roof because I saved the best spot for my PV panels. Think that through. Now's the time. Maybe your new panels shouldn't even go where the old ones are now. I don't pay for electricity any more (PV paid for itself by now), so I don't pay anything to heat my pool, either. If this is your forever home, every day is a better day than the next to invest in PV solar.
And finally, I installed my panels myself and know for a fact I did a better job than any contractor would have. I saved about $7K doing it myself. I learned how best to do it from the local contractor that sold me the panels at an incredible price, and this website. They have some great tutorials along with illustrations that really helped me understand solar heating. I'm very handy, so there is some skill involved, but it is possible to DIY.
Detailed plumbing and operating instructions of solar swimming pool heaters.
www.h2otsun.com