Hello,
Since you've already done the hard-work, and if not possible to do what urkexia suggested, then I suggest you upload them separately. You can only upload as version 2 (V2) if you were the original uploader. Or an admin can do it, but that is just too many seasons and episodes for us to dedicate the time for by going through them individually.
Best and fastest method:
After you have uploaded them, create a report to the admins so they can delete all the machine trannies instead.
Thank you for your hard-work.
PS:
If you've only transcribed season 1, it will be faster to rip the official versions, if you can. If you're not able to do that instead, no problem.
PPS:
I just noticed season 1 was uploaded by you originally, you can update your own subs as V2 yourself. Click edit, then:
Sub Filename CD1 (update) : (click on that "update" button and select the new file).