Your best shot is with verifying the correct orders and assignments from The Movie Database and TheTVDb. It appears there’s some slight differences between the two:
Mini Series
TMDb has listed the mini series as a separate show while TVDb is listing it as specials of the main show (s00e01, s00e02).
Blood & Chrome
TMDb has listed Blood & Chrome as a standalone show while TVDb is listing the webisodes as single special episode (s00e40)
Razor
Razor has an easy and a more complicated part 
Webisodes
The webisodes are listed as specials of the main show on both repositories – though as different episodes
| Episode | TMDb | TVDb |
|---|---|---|
| Day 4,571 | s00e12 | s00e33 |
| The Hangar | s00e13 | s00e34 |
| Operation Raptor Talon | s00e14 | s00e35 |
| Free Fall | s00e15 | s00e36 |
| The Lab | s00e16 | s00e37 |
| Survivors | s00e17 | s00e38 |
| Escape | s00e18 | s00e39 |
“Main event”
TVDb is listing the the “main event” as a 2-part special (s00e04 + s00e05) while TMDb is listing it as a movie
The Resistance
Same as with Razor, the webisodes of The Resistance are listed as specials of the main show – again with different episode numbers
| Episode | TMDb | TVDb |
|---|---|---|
| #1 | s00e02 | s00e23 |
| #2 | s00e03 | s00e24 |
| #3 | s00e04 | s00e25 |
| #4 | s00e05 | s00e26 |
| #5 | s00e06 | s00e27 |
| #6 | s00e07 | s00e28 |
| #7 | s00e08 | s00e29 |
| #8 | s00e09 | s00e30 |
| #9 | s00e10 | s00e31 |
| #10 | s00e11 | s00e32 |
The Plan
Similar to the Razor “main event”, The Plan is listed as a movie on TMDb but as a special on TVDb (s00e22).
Long story short… you’ve got quite a project
Start with verifying which schema best meets your files and how you want to organize the show – e.g. if the Razor main event is a single file it might be best to follow The Movie Database’s structure by listing it as their separate movie – if you’ve got the files as 2 45-minute episodes it might be easier to use TheTVDb as your reference. There’s no objective truth as the community on each repository will claim their’s is the gold standard
Once you decided, rename your files and re-add them to your library.
Edit: reworked the formatting
