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What is the red dot that is seen on the live rock? this is new setup just a couple of days old. I cant say for sure if it was there before I put in the tank.
Also in this rock, I see a large gray colored stuff. It looks like thick dust on the rock. It is not visible in the picture; is this rock need to be cleaned? This is a base rock.
I would say it looks coraline algae as well. It is a good sign that your tank is doing well. To be sure, gently rub it a little, if it comes off and is sort of "powdery" it is probably not coraline, if it stays in place it is.
The first picture is simply the start of coralline. Good stuff. You probably have diatoms or detritus on your rocks in the second picture. Take a turkey baster or ph and blow it off. I blow the dust off my rocks right before a water change.
Is there a specific way that I should arrange the live rocks? Should I put base rock in the bottom and seed rock on top as many would suggest? I particularly like some of the base rocks so is it ok to put them on top of the seed rock?
What ever you like.. Set the tank up so it looks good and leaves room for fish to swim and a place to put corals.
I don't think there are any scientific reports out there that say you need to have LR on top of base.
yep, the reason LR on top is usually recommended is because it looks better, and putting LR on the sand will somewhat negate the surface area on the bottom for filtration. But do what looks good to you. You might browse some tank pics for ideas.