"popup" is definitely not the right
word.
1) I don't know what you mean by "generic holder", or even holder. A <div> is a way to create a block of elements to be dealt with as a
unit, so I think the answer is "individual" even if I'm not quite sure what the question is.
2) Again, not clear what the question is, but I suspect the answer is to just keep track of the appropriate z-indexes.
3) Page level vs CSS level? Does not compute. What are you meaning?