So, when you put D5 on piano roll it will be really the A4 sound on the piano. Especially with samples the piano roll can be a bit confusing - for example you can use recorded sample of the G4 sound on the piano, but when the sample is loaded it is as default treated as C5 note. I don't know what instruments/synths/samples you are using. It's hard to answer your question for 100% because it's very broad. (BTW in piano roll menu in the top left corner there's useful Stamp tool that makes using scales much easier and you can start from any note). C notes are marked just for convenience as in the music C is usually used as point to which everything else relates. If you look at the piano roll you have full chromatic keyboard with all the notes.
FL Studio does not force you to use C scale.
