When I write out the chord on the staff do I note the 5th as Db or a C#? Does it matter?
If this is the fifth of the F♯(♭9) chord, then you would want to notate this as a C♯. This is because the fifth of the chord is so named because it is a fifth above the root. Since the root is some kind of F, the fifth must be spelled as some kind of C. The D♭ is enharmonically equivalent to this C♯, but technically speaking the fifth is C♯, not D♭ (which would be a sixth or thirteenth of some kind).
Also I am looking at the Ab altered as a tritone sub of D7 in G major. Should this be written as Ab or G#?
You would spell it as A♭. Since this chord will typically resolve to G, it will be easier to notate A♭ moving to G instead of having to move from G♯ to G♮ (with all of the natural signs to remind the performer not to play G♯). Furthermore, the G♯ chord would involve a B♯, and although this won't bother any performer worth their salt, it's typically better to notate music in as friendly a way as possible when there are multiple options.