Make the files for the videos and subtitles match per-episode (i.e. s01e01.mkv and s01e01.srt) and VLC should use the subtitles automatically.
Or you can sub to CrunchyRoll if that's available where you are and it apparently has the original Japanese version with the 2 episodes not dubbed in English, and they are subtitled there as well.
3
Where can I find the Samurai Pizza Cats series with subtitles? | Spyke
I've not personally tested this as that would be time consuming, but here (English audio):
Archive Link 1 Archive Link 2
English subtitles (they kind of make it a pain to download but I couldn't find another source). You could instead try using software that generates the subtitles for you, but I don't have experience with any of those.
Make the files for the videos and subtitles match per-episode (i.e. s01e01.mkv and s01e01.srt) and VLC should use the subtitles automatically.
Or you can sub to CrunchyRoll if that's available where you are and it apparently has the original Japanese version with the 2 episodes not dubbed in English, and they are subtitled there as well.