Backup without duplicating files already on hard drive

Apologies in advance for quite newbie question..

I have previously manually copied and pasted whole folders like Desktop, Downloads, Documents etc to a portable hard drive.

However, I've gone to do this process again (where I've wanted to override all the files on the hard drive in case I've updated them om laptop since then) but it says one of these folder transfers is going to take a day (not sure this is right as don't believe it took this long last time but anyway..).

I've now learnt you can use the Windows back up tools to do this. I'm just concerned that if I do this it will transfer the files under a new folder in the hard drive separately to the files I already have on there (do not have space for both). Is there a way I can stop backup from doing this and only backup files not already on the hard drive?