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You can make your mod to one BSA the same format as the game it self are.
General rule is dont extract the BSA. If you dont know what you are doing and not using MO.
Some mods are fine to extract and others are big NO NO, like The Unofficial Patches and Usleep.
If you have one mod that have lose files and you have the same file in the BSA then the lose file will win and will be loaded first. Since it goes faster.
Some reading for you
https://forums.nexusmods.com/index.php?/topic/5416190-bsa-and-loose/
https://www.reddit.com/r/skyrimmods/comments/5fknwv/whats_the_difference_between_loose_files_and_bsa/?st=j9uuotl1&sh=f096efdf
http://forum.step-project.com/topic/3668-loose-vs-bsa-files/
BSA files are archives containing various types of content, such as meshes, textures, sounds, and so on. When you activate a plugin, the game will look for a BSA with the same name, and make use of its content if one is found.
An alternative to using BSAs is to simply dump the content files directly into one's Data folder. Some mod makers don't distribute BSAs, and only include their content in this "loose" form. Some mod users like to extract these files from the BSAs they download, in the belief they'll have a more stable / faster game.
Accepted wisdom is that all BSAs load faster, though some use compression - this lowers their size on disk, but increases the horsepower the game needs to read through them while playing. For some players, in very rare instances, this is a problem.
On the other hand, with loose files, load order becomes a serious issue: loose files always override anything found in any BSA, even if the mod they belong to isn't even active within your plugin load order! Worse still, extracting multiple mods into your Data folder that happen to use files with the same names will result in overwrites!
Mod Organiser is worth noting in that it takes special control over your load order, meaning that it can eg force the game to use the files in a BSA instead of loose versions. However, as a general rule of thumb, there's seldom a good reason to use loose files when BSAs are provided to you.