I went through this just last night. I "remade" all my cue files (made blank zero byte files and just named them "gamename.cue"). However the scraper scraped the same game over and over again and the game was for the sega megadrive not the psx sooooo shrugs
You can add the videos manually yes. Place them into your /home/pi/RetroPie/roms/psx/images and then re-scrape them. Two things though..
your videos need to be renamed so they have -video.mp4 on the end (i.e. Tekken (USA)-video.mp4) I would strongly suggest you use a batch re-namer to do so! (for windows use Bulk Renemer or for linux use Pyrenamer it is in the repos))
The BIG problem is the two scrapers don't play nice with each other. The "built in scraper for ES will delete the video tags and Steven's scraper may not pick up the correct info due ti the database (I guess).
So what happens is you don't get boxart or info and the wrong vid but everything is tagged...then you go trough and redo them and you get boxart and info but no tags. I have not tried to scrape the videos locally from the folder after using the built ES scraper yet. It might not erase anything and add the video tags.
So you want to do the built in ES scraper first and then use Steven's scraper to scrape from your folder after you have renamed all your videos. I can try that later and see it it works..but again you will need files that at least end in the correct extension. I had I batch/script that would do just that..but that was a lifetime ago when i was using MameWah..I'll see if I can dig it up...but don't hold your breath ;)
Edit: Ok so here is what i did..and it worked..okay...
I scraped all my pbp files with the built in scraper then I used Steven's scraper scraping just the cue files and append that to my list and it scraped some of my videos. So I still had to hand edit my list..so might be the only why do to it is by hand..
Here is an Idea..scrape just the cue files (making sure thy have the correct name and all that) with the built in first...then scrape with Steven's scraper appending the information to the list (that way your video tags are added) last go and do a find and replace on the gamelist.xml and search for .cue< replace with .pbp<
(yes add the less-than sign..just to make it harder to replace something else.)
The only catch with that is your pbp will have to match your .cue file names exactly it's an idea anyway.
EDIT: You can batch rename your .pbp to .cue then scrape..then rename them back from .cue to .pbp