Your source water is the foundation of your system. Using well water can be all out dangerous to your reef if you're oblivious to the quality. Depending on where you are, how deep your well and many other factors, you could be dealing with pesticides, toxins, heavy metals and a bunch of other nasty stuff not normally found in tap water. Typically well water is not near the quality of tap water. Combine that with no TDS meters, not enough stages in your filtration system, and lack of frequent enough cartridge changes (because you have no TDS meters to tell you when they need replacing) you're setting yourself up for continued issues. Its imperative that you know exactly what you're dealing with as far as water quality PRE filtration, as well as post (final water quality). If you don't know exactly, you can't eliminate it as a potential problem. Educate yourself thoroughly on your specific well water quality and then develop a game plan for filtration and usage. Start by testing for CO2 and send out a sample for a very thorough test including heavy metals and chemicals.
My RO/DI is 6 stage. I set it up to run well water through it. My well is high in CO2 so I have to aerate it prior to filtering. It is heavy in iron. I go through the first stage cartridges (sediment) very quickly. It got to the point it didn't pay to use well because of how fast I went through cartridges and the extra effort it took to perk the water prior to filtering. So i went back to tap. At some point I may revisit using well but right now it's just not worth it.