It does matter where you put alternate glyphs, though within the Private Use Area you can map them any way that you wish. I wouldn’t recommend using the Coptic character set. It will confuse users who use your fonts with Coptic characters and it prevents you from adding Coptic characters to your fonts, should you ever wish to do so.
If you’re using VOLT then they don’t need to be mapped at all (take a look at Palatino Linotype, for example), but as you say that you have no applications that support OpenType features then they do need to be mapped or they cannot be used.
FontCreator assigns the following Private Use Area codepoints for use with Small Capitals, Stacking Fractions, Old Style Numerals, and Ligatures:
58033-58126 Basic Latin Small Capitals
58161-58255 Latin-1 Supplement Small Capitals
58256-58383 Latin Extended-A Small Capitals
58384-58591 Latin Extended-B Small Capitals
58912-58974 Basic Greek Small Capitals
59072-59218 Cyrillic Small Capitals
59680-59829 Latin Extended Additional Small Capitals
60531-60542 Number Forms, Nut Fractions or Stacking Fractions
61125-61148 Selected Ligatures from the Medieval Unicode Font Initiative
All values are in decimal notation since the Complete Composites feature data file uses decimal codepoints.
The Medieval Unicode Font Initiative is an extensive proposal to the Unicode Consortium for inclusion of additional codepoints. FontCreator includes definitions for some of these. It may save some work to use the Transform Scripts to add the ligatures to your fonts, then the mappings will be done for you.
See my tutorial on Customising Unicode Data for some insight into how the Private Use Area is currently allocated.
The standard Unicode data text file distributed with FontCreator does not include these non-standard definitions in the Private Use Area. Mappings in the PUA had to be assigned in order to make Complete Composites and Transform scripts work at all, and to use these extended features in applications that do not support OpenType features.