Take a look at the Vietnamese Glyph Transformation and run it on a standad font to see how it works.
From the Insert Characters dialogue you can insert up to 1,000 characers at a time with the correct mappings, simply by pasting code-points from a text file.
For example, try pasting this text into the Insert Characters dialogue:
32-126,160-383,402,416,417,431,432,461-493,496,500,501,504-539,542,543,550-563,702-703,710-719,728-733,755,759,768-785,795,803-806,813-818,937,960,7680-7835,7840-7929,8208-8231,8240,8242,8243,8258-8260,8268-8270,8273-8275,8304,8305,8308-8334,8352-8366,8448,8451,8453,8454,8457,8470,8471,8480-8482,8486,8487,8490,8491,8494,8507,8531-8543,8706,8710,8719,8721,8722,8725,8729-8732,8734,8747-8748,8756-8758,8764,8776,8800,8804,8805,57344-57364,64256,64259
Are you working with CJK fonts? How many characters do you need to map?
Also take a look at copying a range of glyphs in one font from the glyph overview, and pasting the mappings to emtpy glyphs in another font with paste special, (mappings and postscript names, not glyph outlines).