I think this will be a noob question but how can I pack my mod to BSA file. I have created new scripts and things and when I want to upload it comes this problem. Packing them. If some one can help me it will be great. Thanks in advance.

Select "Upload to Skyrim Workshop" and it will offer to pack files for you.
At the end of the process, even if you cancel before uploading, you will have an esp and a bsa file in your Skyrim\Data folder.

Not sure why everyone says to upload to the workshop. All I do is go to file--->create archive, then drag the files I want to be included into the window, and hit pack files. (Note: the files need to be placed appropriately within Skyrim's folder structures, such as placing new texture files into Data\Textures before adding them to the archive). I believe the archive is created once you click on "pack files", however I usually save right after that for good measure.

I don't know if it's been fixed in one of the patches, but the "Create Archive" didn't work before. That's probably why everyone says upload to the workshop

I've also got some questions regarding this. Do I need to link my .esp to my archive in order to get it working? Or does Skyrim (and plugins) automatically read/have access to everything within the Data folder, also meaning .bsa-files? For example, if I create a script "HelloWorldScript" and then add it to an archive and put that archive in the Data-folder. Could I remove the "HelloWorldScript.pex" from the Data/Scripts and the script would still be working because it is found in the .bsa?

Edit: I made a small test. I added a fragment to a quest (which created a TIF_010079D0 script). I then went to File>Create Archive and added this script (already compiled, as a .pex). I then removed the orginal file from Data/Scripts but added the archive instead. However, when I try to edit properties it says "Cannot open store for class "TIF_010079D0", missing file? Am I doing something wrong?

I am asking since I'm working on a plugin with a friend of mine. We are only working in the CK one at a time and so far it has been enough just to copy the esp. With the addition of quests and scripts though we seem to have run into a problem since the scripts are missing despite our archives... is there any simple way of testing if the archives work?

Edit: We managed to solve the problem. I didn't realize that the creation kit doesn't access the archives (so when playing the mod with the correct archives everything works out fine). When using the CK we just have to manually copy all of the scripts.