I currently have 4 domains hosted through GoDaddy Classic. 3 of the four have all files living inside a corresponding folder in Files. The 4th is one that I forget to put inside of a folder and have built out over the last 5 months. It is a WP site with all corresponding data/files currently inhabiting the root folder. This creates a lot of confusion and is messy.
Can I just create a folder and move all the data/files into that folder or will it disrupt the functionality of the site?
Yes + if this type of activity is new to you, I'd suggest you do the following.
1) Setup your folder for your new site.
2) Change your Apache config to point your DocumentRoot to new folder.
3) At this point you should see an empty folder serving.
4) Now... very carefully, move files out of top level directory into new directory.