It mostly depends on what you want the bass note to be. A good idea might be to play all different inversions in the progression and really listen to how each inversion sounds in the progression. Does one give a more distinct sound? why? how? Does one make the cadence ( the V - I ) sound weaker? why do you think?
This will also help alot in two ways 1) in the future you will know what inversion because you'll know how it sounds, 2) you'll be able to hear which inversions other songs are using and thereby better understand how other musicians are using inversions... that is, if you really spend time listening (and singing) to how the inversions sound, and how they sound in a progression.
So... the correct one to choose is the one that sounds best in that situation. Unfortunately that's not a very solid answer, but it's true... different inversions go better in different situations. Try them out and see.
As for a standard rule of thumb... keeping them in root position will give you a stronger sense of the chord changes, inversions should be kept to a minimum, and they work best when the bass note of the inversion is a passing note (between 2 root position chords - ex: C G/D e). But, these are generalities from theory class... which means they don't have all too much application in real life other than "it worked well to do it like that in the past", which makes it a safe bet.