Once I have cloned C: to D: , will I have a boot menu after powering on the PC asking me which HDD to boot from? Will windows create this boot menu automatically?Not necessarily. And it is better when you do not get this prompt. Because the record about the second drive is set in bcd and you want an exact copy.
I don't know about incremental copy but this tool can definitely clone a HDD, even on schedule basis: https://www.paragon-software.com/home/dc-professional/features.html
If incremental copy is important then as an alternative you could use backup with Full+inc+inc+inc chains.