Some mods, when added, bring up a message - "this archive contains plugins in subdirectories, and will need a script attatched for FOMM to install it correctly". What should I do here?
In short, you should either 1) extract the mod to a temporary folder before fomoding, customize it to your desire, then fomod the custom folder rather than the original archive; 2) if you want to use the default settings for the mod (assuming it has them), ignore the message; or 3) learn to write a fomod installation script and add it to the fomod of the original archive.
Detail: This message means exactly what it says, but if you're not familiar with how the game engine reads/accesses files, it may be a bit murky.
1. The game only reads ESM/ESP files directly in the Data folder, and resource files from folders with specific names inside the Data folder (such as "Meshes", "Textures", "Sounds", "Video", etc.).
2. If a mod archive converted to a fomod contains "invalid game folders" (folders that the game won't look inside because they don't conform to any of the folder names that the game recognizes), and those invalid game folders contain alternate or compatibility ESM/ESP files, when activating the fomod (which is essentially the same thing as extracting the original archive to the Data folder), these invalid folders will be replicated inside the Data folder, meaning that if you want to use the ESM/P inside the invalid folder in place of, or in addition to the 'default' ESM/ESP, the game won't be able to "see" it (because it's in an invalid game folder that the game ignores).
3. To resolve this issue (if it needs resolving; you may not want to use any of the alternate ESPs for any particular mod), the alternate files must either be moved to the root folder of the pre-fomod archive/extraction folder (taken out of the "options" folder and moved to the main folder where the textures and meshes folders and whatnot live), or, if you don't want to pre-extract the archive and customize it prior to using "add from folder" in the fomod creator rather than "add from archive", an installation script must be written (I believe FOMM scripting uses C##) to tell the installer to copy specified files from the invalid folder inside the fomod to the data folder, rather than just extracting it to the invalid folder as it would normally do.
But whether you need to do any of that depends on the mod itself, what extra/optional files it contains, and whether or not you want to use any of said optional files.
Hope this helps.