If the accents are not being generated automatically, perhaps the mappings are incorrect, or there is some other problem I don’t know about. If you can attach the font, then I can see what the problem is.
If you use simple glyphs you will lose all the benefits of using composites (easier editing, smaller file size, etc.)
If you need different accents for lowercase/uppercase, this can be achieved automatically by creating low profile diacritics for uppercase in the Private Use Area.
The design is up to you — I call them low-profile because they are designed to save space above capital letters, but they could be bigger then regular (lowercase) accents if that’s what your design requires.