The DS can't handle formats such as .lit or .pdf which means you are stuck with .txt which actually ist no problem at all.
Just remember to use Unicode (UTF-8) or Westeuropean (Windows, works well for me) as coding when you save your .txt (in MS Word for example).
I recommend "ReadMore", an excellent Homebrew to read on the DS, DS Reader is nice, too. Both provide you with a bookmark option which comes in handy. DS Reader has a few snares there, though.
You can copy your files into a folder of your choice (apart from _system_ and moonshl ;-) and search them after starting the program.
Bookmarks