I think most people will tell you to break up the single unit of 3 into 2 units. They might also tell you that 2 units of 3 is overkill and a waste of points due to the diminishing returns. This depends on the rest of your army. With a saurus army, using that many points on salamanders might not be the best tactic because this will cause your saurus units to be smaller. However, with a skink army it might be ok.
To answer the other part of your question: I run my salamander units next to one another on a flank. I know most people say that they prefer to have them away from one another so they can focus on different units and force more panic tests, which I think is a sound tactic, however my personal experience makes me disagree.
With the new BSB re-roll rules, I find it rare that my opponent runs from the panic caused by the salamanders. Also, there are a lot of races and units that are immune to psychology, which negates the panic ability of the fireball. This is where I like to have a lot of salamanders to just kill stuff, and not worry about psychology.
I do however like what a some people are doing. Running 2 units of 2 with extra handlers. This offers a good balance between point cost, panic tests, killing ability, and not having to take a monster reaction test. I would start with that technique until you get a feel for your army and the salamander strategy. Good luck.