Buckey,
What your pool guy told you is a load of Bull Feathers..
The truth is that pool guys just dump in all kinds of stuff that we don't recommend and some of it does not go away.. But you can't tell just by looking at the pool, you have to test the water to see what "balance" it is in. This is really what TFP is all about. We teach pool owners how to test their water and let the pool owners decide what the pool needs and more importantly what the pool does not need.
If your pool guy has been using chlorine tablets to sanitize your pool, it is quite possible that the CYA (Stabilizer) could be very high. The higher the CYA the harder it is to keep the right amount of chlorine in the pool.
The only way to know is to test the water. If you test, you want the testing to be accurate and we find that test strip and pool store testing leaves a lot to be desired.
I suggest that you buy your own test kit.. Either a TF-Pro from TFTestkits.net or a Taylor K2206C. The "C" is important, so don't buy one without it.
No matter what you do, I suggest that you don't drain the pool until you have some kind of testing done.
Most IntelliFlo pump manuals have a "Menus" page.. I find it is easier to understand how the pump works by looking at the Menu page in the manual first. It kind of gives you an overview of what goes where. If you use the Menu page you can look at what setting are already in the pump.
As far as your valves go, I'd leave them as they are for now. I am not a big fan of In Floor Cleaning Systems (IFCS) and if this were my pool I'd most likely shut it off. That said, this is your pool and you should evaluate how well the cleaner is working first. If you think it is doing a great job, just leave it on..
Thanks,
Jim R.