As far as I understand when we are in x86 Real Mode the first megabyte memory layot looks like that:
Will memory layot be changed once we jump to Protected Mode? I know that we can access video memory by the same address like we did it the Real Mode but what about other regions? Can we overwrite them? I suppose we don't need the IVT and the boot sector anymore. But I'm not sure about others.
Short answer: No.
Long answer: The layout of memory does not change depending on what mode you are in. However, when not in real mode, most of the memory in that region is irrelevant to you, and can be used. However, you must know that a LOT of memory in that region may be IO-mapped, and thus, it is a good idea to load your kernel >1M (2M is the optimal place) and to ignore the first 1M of memory.
Once you implement paging and page allocation, you will want to reserve the first megabyte of memory, thus not allowing it to be allocated.