I am struggling to see a difference between the following (with P being place and N being noun):
P に N が あります。
N は P に あります。
They seem to both be “N is in P.” Or no? Please help me 
They are both about the same in terms of meaning, with a few exceptions dealing with which information has higher priority in the sentence. There is a link on imabi somewhere, I’ll see if I can find it quick.
[edit] Link: http://www.imabi.net/10majoraspects.htm
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It changes what you’re emphasizing. This isn’t exact, but it’s that kind of thing.
There’s a _____ in the _____. (and not something else)
In the _____ there’s a _____. (rather than somewhere else)
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I was reading Jay Rubin Making sense of Japanese, and from what I remember ha sends the emphasis forward and ga throws it backwards onto the thing that preceded it.
So, ここにぺんがあります。The PEN is here.
Or, ぺんはここにあります。The pen is HERE.
This is a really simplified example and this is totally contextual as always but I recommend Rubin’s book if you want to know more about wa vs ga, which is as hard for English speakers as a and the is for Japanese speaker… and let me tell you they have trouble with a and the.
@Leebo, let me know if I’m totally wrong. It seems like my explanation fits with yours, just another way to say it.
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