I've done both myself before as well, and personally I like the first method best using TESArchive. The Creation Kit can be buggy as a duck and doesn't always show what files you put into it even though it should or sometimes doesn't let you (it really sucks when you have a lot of loose files from mods over a long period of time and is rather time consuming at best). As with TESArchive, its much more stable and gives detail to what you're putting into your archive. An alternative to drag and drop, you could just click the Edit menu and select Add directory, or Add file and it will load up a specific file or a complete directory with every file in it (saves the headache of looking up each one). In saving, sometimes you have to exercise patience because after you start saving it wil say "writing file data to temporary file" on the bottom (I'm guessing this is part of the bsl file process), it may seem like it's stuck, but really its working out all the compression and file retaining structures you've associated with it, depending on how big or how many files you've included determines it's file size (some of my loose files are 5Gb just in texture files). Whatever you do, leave it alone and don't close it or even click anything on it. Usually its done when you see "Renaming temporary archive", just open up windows explorer to see if it's in your skyrim data folder (hopefully you choose to save there), then its safe to close the program. Now for getting the game to use your newly created archive is another additional step that I found you should do and no you don't necessarily need an .esp file to get it to work. Edit your skyrim.ini file located in "My Documents\My Games\Skyrim" using notepad or preferrably notepad++. Scroll down to where you see [Archive] and under the line "sResourceArchiveList2" add your bsa file name followed by its extension and yes its case sensitive, so word for word, letter for letter. I suppose you could use the first sResourceArchiveList, however, I feel its probably best to leave that for the base game, not mod extensions. This secondary list is very useful for bsa files from the DLC as well and would recommend adding them there too. Save your changes, then bring up the file properties on the skyrim.ini file and on the General tab, find "attributes" on the bottom and check the box indicating "read only" then click OK. The purpose for this is so that we're preventing the launcher from making reverting changes automatically should you wish to alter you mod list or graphics options. Launch your game to see if everything checks out ok. If everything seems to play out ok, I suppose you could take the file folders that have the loose files and temporarily move them to your desktop or external drive, then launch the game again to see if everything is still performing the way it should. If all goes well without the loose files, don't delete them just yet. I would suggest compressing them in a zip or 7z or something as a backup just in case something goes wrong so that you can restore your game without losing your library of loose file mods. There's nothing worse than not being able to find an old mod you liked that had been a part of your game and now is lost to the digital oblivion gates in the sky. Hopefully this helps.
