Welcome aboard!
I'm pretty sure that just getting a "folder already added" alert is not a problem, it's just letting you know that the new mod wants to create a folder that another mod already created. Which should not be an issue, if the necessary folder is already there the new mod's files for that folder will just be added to it.
What you really need to look out for are the notices that a particular
file that another mod added or changed is going to be overwritten - if you don't already expect it and know it's not an issue, time to stop and investigate further.
