Let me say right off, I much prefer a Clean Install when Moving from a HDD to a SSD.
But sometimes it's just not practicial, SO:
1) Yes it will still be there.
2) How big is your "C" drive, Not so much total size, but used space?
3) On My Wifes' system; Just used EZ Gig IV (Note version IV is a free down load if you got ver II).
.. It did a great job.
A) It enabled Trim
B) It placed the System partition On the SSD
C) And the Alignment was OK.
What I did in prep for the Cloning.
1) I verified the HDD was set up using AHCI, mine was. BUT if Your windows on the HDD was installed with the BIOS set to IDE, The FIRST Fix it, switch it to AHCI.
.. You can not just go into bios and change, if you do it will prevent you from booting into windows. Google "ide to ahci windows 7" for instruction.
2) I ALWAYS partition My HDDs - C Is for OS + Programs and D (or other partitions) are for MY data.
.. Her partition for C drive was a little larger than the SSD, So I shrank it using windows disk management. You do Not need to do this, EZ Gig will check "used" space on Old HDD and Space on the New SSD. It will partition accordingly. If files on "C"-drive take up to much space you will have to decide on what to take over and what to leave behind.
After clonning, based on your system, you should be able to Daul boot untill you delete windows on old HDD. My Wifes system still has windows 7 on the HDD. Boot priority i set to SSD. If she needs to use windows from the HDD, all she has to do is hit F12 during the post. When Post completes, a Boot menu pops up and she can select which Hard drive to boot from. Which ever drive is selected becomes the C-drive. Rebooting auto reverts back to the SSD unless F12 is again Hit.
Once you are satisfied that SSD is runing smooth, you can ditch it.
Read up on tweaks that help keep your SSD runing smooth.