Servers that have rebranded will stay in their respective folders. For example, Toontown Offline logos will be stored in the Toontown Realms folder. The same can be said for Toontown: Corporate Clash and its former Toontown: Project Altis alias.
Be sure to label any logo you find with a rough idea of when it was used. Doesn't have to be specific, but extra information would be nice. The more the merrier, really.
Only try to upload logos from official sources, with the exception of backed up copies found throughout Archive.org. If the logo looks blurry and has a white background, then chances are it is not official. These can be sourced from websites such as DeviantArt providing they are uploaded by the logo artist themselves.
Unused logos (that were completed) are also welcome, but I request that you place them into an additional "unused" folder i.e. Toontown Rewritten/Unused.