So far, I have tried doing Roman numeral analysis mainly on Classical- and Romantic- era music. However, I just took a look at some Miles Davis, and didn't know what to do - there were so many chords which, regardless of how you analyzed them, would contain a handful of 9ths, 7ths, 11ths, and 13ths. When you're dealing with such music, how do you decide what the optimal analysis is? For instance, if [D-C-E-Bb-G] could be a Cdom7/9 in inversion or a E-half-dim/13 in inversion, how do you decide which analysis to choose?
What you should first look at is how the chord is functioning. For example, if it's leading to an F chord, then it's probably C9; if it's leading to an A chord then it's probably Em7b5.
I do wonder where your example came from, though. Other than dim7 chords (which are usually just dominant chords without a root), third- and especially fourth-inversion chords are not very common in modern popular styles of music. Certainly the bass note being the 9th of the chord would not be my first assumption, so if this is occurring frequently in professionally produced music, I would explore other possibilities first (like maybe I got the wrong notes).
By the way, jazz is extremely heavy on modern music theory. Just slapping down a couple of ii7 notations is not going to work for greats like Miles Davis. You will find a lot of chord substitutions, quite a bit of modality, and even some atonality. A lot of your classical theory training will apply, but some jazz music (especially from the Bebop era onward) will challenge the rules you learned. It's best to use it as a foundation from which to move on to jazz theory, rather than something that can be applied directly.