Zac -
Finale's method of having trills play back is cumbersone at best (and I'm being polite here). What I found the works really well is to:1. Notate the trills as you want them to be read in your score;
2. add a staff (or staves) at the bottom of your score and set it up in your Instrument List as Flute (or whatever inst you want);
3. write out your trills on the added staff as individual notes (32nds, 64ths, or some type of tuplets) as you want them to sound;
4. Hide the "extra" staff with the trills which will play back;
5. mute the visible flute staff at the top of the score.
Seems like a lot of work, but it's really less than what Coda has built in.
Good luck!
-- Dan