It's been months since I've last converted an anime episode to watch on my PSP, but I do recall being fed up with PSPVideo9. XVid4PSP was much better interface and had quite a few more options for me I preferred. Anyway, I remember I used one of the MKV tools to rip the subs from mkvs and inserted the subs that were extracted with the Subtitle tab you see on XVid4PSP. Not sure what you mean by hardcode but ever since I've used MKVtoolnix with MKVExtractGui in it, I've been able to watch all mkvs subbed fine on my PSP. My bad if this didn't help.
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