If you restore configuration files that reference themes layout or whatever you didn’t install first, then this will probably create issues by not finding what is referenced in the config files. If it is a wallpaper, the impact will be minimal, but for some bigger component like a whole desktop theme, then you’ll probably break your user desktop. For non desktop related config files, then it is non really a problem, for example your desktop will not crash if you have your VLC config files before installating VLC, but for the desktop itself you need to be careful (and logic).
I think you would need to install everything first, then logout of user, copy (and/or overwrite) the config files to your user folder, and then log back in to the user. If everything is where it is supposed to be, everything installed like before, you should not have issues.