You don't need SPON Core twice. You can happily use SPON Map with the ACE mod and it will use the Core it finds there. You'd need to ensure that the Map addon was loaded after ACE though, or it will complain that Core can't be found.
You could reorganise the list, I think, by creating a replacement addon that redefined all the markers. However, if you reorganise the list, you won't be able to access the ones that are easiest to access now ;P Certainly, if you are playing ACE, you can't avoid having a ridiculous number of markers, making the standard selection method quite unwieldy.