I used to do this regularly. Then one day I looked at my data folder and realized it was a total [censored] mess. Everything worked in game just fine, but trying to figure out what needed to be uninstalled and what needed to stay was a nightmare. In the end the best option simply was to nuke the whole damned thing and start over from scratch.
Back then, trying to figure out Wrye wasn't exactly a pleasant experience. I don't remember having the sorts of videos out then, that we do now, on how it functions. Took me what seemed like forever to actually figure out just how it works, and how to manage my mods properly.
But yes, it is definitely a good idea to know how to install manually, but IMO it is more important to learn how to use Wrye, NMM, Mod Organizer, the like, efficiently early, rather than waiting till you have to nuke your entire install later. You'll save yourself a huge headache in the long run that way.