As far apart as possible and even then they will likely interfere with each other especially in deeper water. You can put one on the bow and one on the stern and it will work okay in shallower water (less than 20 feet or so). I read an article on this topic last year but I can't seem to find it now. I ignored the advice it gave, tried it, and failed. There are different transducers you can buy with narrower beam angles too which would help. I am sure there is a way you can make it work for shallow water at least since lots of guys do it on bass boats. Josh at Angler Outfitters knows all the ins and out on this topic as well.
If they run on the same MgHZ interference is a given. You can only use one at a time. If you can get a transducer with a different MgHZ than the other one you can run both at the same time. I had 2 lowrance units on my charter boat and ran into this problem. I sold one of the units and purchased a different brand and could run both at the same time with no interfence.
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