I have almost completed a small quest mod and I understand how to create a .bsa file and an archive to upload to the Nexus. My question is does the .seq file get packed into the bsa, or should it be uploaded with the archive or as a separate file?

Yes, you can/should include the SEQ file in the BSA.

Interesting. I tried that last time I packed up a mod. I couldn't get Archive.exe to accept the seq file. I expect I missed out a box that needed ticking...

You may also try to avoid the SEQ requirement if you want.

You know, the SEQ file is required if you set the quest as "start with game". You can make a quest that have the "start with game" flag and it have a stage where it starts the quest related to the dialogues.

On my specific case, I'm working on a mod that have the story manager that trigger a "preparing quest" and this one have a stage that starts the dialogue quest.