Yes the way you have written means you are STILL thinking about "it". This is present perfect continuous. If you have stopped thinking about 'it' at this moment you can use the past perfect conditional. This would be, "I HAD been thinking about it all day" Hope this helps!

I think, verb "think,understand, like" doesn't use in present perfect cont. I've thought about it all time.

There's a slight error in the second part of your sentence. "I have been thinking about it all day, and I AM still thinking". Apart from that, it is fine, and natural. Using present perfect continuous already includes the meaning of 'I am still...', but you can certainly add that as emphasis. If you are not still thinking, there are a couple of options. You could say 'I had been thinking about it all day', or 'I had thought about it all day'. The first one is better if you are going to introduce something that ended the thinking. e.g. I had been thinking about it all day, until I finally made a decision over dinner'.

A more natural way would be to say “I thought about it all day”. This implies that you spent all day thinking about it, but you are no longer thinking about it. As examples: I thought about it all day and have finally made a decision. I thought about it all day, but it was making me stressed so I stopped thinking about it.