Newb question..

[Mhaeric]

It was against Ifrit. I see all these different colored squares on the battlefield with A, B etc.. kept getting messages to stand in them during certain actions from Ifrit to not die. What confuses me is how can you even tell which one to stand in..

Oh, those are player placed markers to help the group know where to stand for certain mechanics. Those are always specific to a fight and sometimes even to a group, since there's occasionally more than one strategy. Watching a guide with an eye for where people need to stand at what time will help you understand what mechanic those markers are there for.

As an aside, people do sometimes use them for fun too so they don't always mean something. That's usually easy to figure out, though, since it does something like spell a word. Most of the time they're there as a party aid, however.