Hi, i recently started playing PPD and I loaded about 15 songs into my game (not from a pack.)
They're all songs with a FT preset but I can only use the D-Pad to alternate notes for overlaps on two of the 15 songs. Why is this? Is it a choice the creator of the notechart made? How can I fix it? The songs are literally impossible to play if I can't use the D-Pad for overlapping notes.

Not sure i got what are overlapping notes, but i guess you'd want to use CSinput mod if you want to play with controller. Some songs might have CSinput script already integrated so that why you can use D-pad there. However, be aware that using CSinput mod will block saving your result in game and uploading it on server.