well pump help needed

I recently purchased a home with an artesian well. I never owned a well before and have some questions about the system. (1) The system was seldom used for the past couple months. I tried flushing the well out by connecting a hose upstream of the filters and letting it run for about 3.5 hours. While flushing the well, the water became very brown, cleared up for about an hour, then became slightly brown. The water coming directly from the well is still slightly brown when observed coming out of the hose. Is this normal? (2) The filtration system consists of two identical tanks with timers on top and a brine tank. Only the second filter is connected to the brine tank. After flushing the well I filled the brine tank with rust stopper salt (the green bag) and manually regenerated both filters at least 5 times. The water after the filters is still brown. Is this normal??? What could the purpose of the first filter tank be??? Do I need to have the system periodically serviced??? Any advice or information is greatly appreciated.

Well I shall try this again, got through my post and somehow it didn't get posted...so here we go again Another newbie here, but have found a tonne of helpful information on this site so thanks to everyone that posts here! I am at the tail end of building my first house on an acreage and in the past few months have learned how to install a complete ducting system, wire a house, install a gas line, do all the drain work and install a pex plumbing system ( its amazing what you can learn when you are way over budget ) Anyways I am down to the last little thing and that is figuring out the proper way to get water from my pressure tank to my hot and cold water manifolds. In my mind it should come out of the pressure tank, which is a 1 1/4 inch threaded hole and then tee off a 3/4 inch line to the hot water tank and then 3/4 inch line to the cold water manifold. Question is what type of materials do I use and where do a tee it off, that is assuming this is correct. I thought I might buy a 1 1/4 inch to 3/4 inch galvanized reducer right off the tank and run 3/4 inch pex but I am thinking that I shouldn't be reducing it that much at the tank. Also is there a rule about how much copper you have to run out of your hot water tank before you can run pex ? I have a three foot piece of copper coming out of the tank and then ran pex from there to my manifold. Does this sound correct ? Any help would be appreciated as I really need a shower and am tired of "going" in the bush :) Thanks in advance