See sections 5, 14, and 15, in the PDF Tutorial Using Glyph Transformations
You don’t need to edit them one by one. Begin by editing the Stacking Diacritics at the end of the font. When you’re satisfied that they’re the right size and position for Capital E then select the Latin Extended Additional characters that use them, make the composite glyphs empty and complete composites to let Font Creator position them again.
See my free fonts such as Garava or Verajja for working examples. When I was designing my fonts, a Vietnamese suggested that the circumflex grave accent worked best if the grave was on the right of the circumflex, not on the left as you have illustrated. You can move it to the left if you wish. Some fonts do that.
See this thread for a tip on adjusting the Geometric Centre of the stacking diacritics that are not symmetrical.
I use various techniques to reduce the height of the stacking diacritics. Otherwise the font’s line-spacing is too high to be useful for normal English text. You can allow more vertical space for your fonts if you wish, as they will be used mainly for Vietnamese.
Format, Settings, Metrics, Maximum, Calculate will make sure that the high accents are not clipped when the fonts are used in Windows applications.