As far as the cloning, a true clone will leave your current drive in tact, it will still be bootable and exactly the same as it is. A clone is essentially a copy. Macrium and Acronis both have a cloning function. The only issue is the SSD alignment which is different than a regular hard drive. Macrium and Acronis will normally work correctly. Paragon Migrate
($19.95) will do the job with no issues, it will transfer and align the SSD correctly. That's what it was made for. You may find this info useful SSD - Install and Transfer the Operating System
As for user files, Windows will by default place your user files in C:/Users/yourusername/ You can move those files to another hard drive easily by User Folders - Change Default Location
or you can place them on another drive and right click them and select include in library and choose the folder in your library you want them in. C:/users/public is, by default kept on the C drive. They are normally the files you have chosen to share with other machines for example. Basically, the files under your user name are accessible only to your user account. Files you have chosen to share are in your user name and in Public.