I would test the water that I intend to use, which generally is the output, not the waste water. I might test the tap water as a sort of sanity test on the test kit itself.
I'm not sure what's killing your membranes, then. A water source with a lot of metals and some carbonate might do that. In that situation, an ion-exchange filter can help, although it might not be worth the cost.
Another question is how much preasure is the booster pump puting out might actualy be to high causing the dammage