First, I would install a line from the water maker to a sink.
(On our boat, there are two spigots, one for the footpumped fresh water; and the second one, for the watermaker in the aft head's sink.)
This is allow you verify by taste and smell that you want to put what's coming out of the watermaker into you tanks. Also, it allows you take this water out and use it as part of the servicing of the tank (purifying, etc.) -- but that's a different subject.
Below the sink we put three valves which tee-off the line from the watermaker, This allows you, by creating a simple manifold with hardware store parts to i) use the sink, ii) put water in one or the other tanks.
We never turn-off the tank to the sink line. If the tank(s) are full, then the water once again comes out of the sink. I wouldn't every "block" the discharge line from the water maker. I was told that creates unacceptable back pressures in the water maker.
Once you commission a water maker, you need to continually and regularly use it; or, service it. You can't just drain it, let it freeze, or not flush it regularly. You need to keep it with a biocide in non-chlorinated water; except when you put the biocide in potable antifreeze, if you keep it winterized. Etc., etc., etc.
YOU NEED TO CHECK THE WATER COMING OUT OF IT BEFORE YOU PUT IN YOUR TANKS.
Water seeks it's own "level". You can cut new holes in your tank (which I wouldn't do; or you can run the lines from the water maker (manifold described above) and tee-them into lines that are from the tanks to your y-valve.