I see on graphs MB, kB and B.
1 MB is 1000 kB or 1024 kB ?
1 kB is 1000 B or 1024 B ?
I found "Base Value" in advanced options for template and custom graph. Is it right place to change bytes value in kB and kB value in MB ?
Yes, you found the right place.
Typically a base of 1024 is used for disk storage and computer memory, however 1000 is typically used when talking about network traffic.