I find that it depends on the bassoon. I learned first to add the low Eb, and sometimes my fingers automatically go there, but I find the tone matches without that key better. I would suggest listening to the difference in the sound between using it and not compared with the D and C and F around the Eb in question and pick the version that seems to match the best. I would say most bassoonists I have met will use the low Eb key, but it's a small minority vote, probably 60/40 in favor of adding the low Eb key.
You should almost always play with the added right hand fingers though (second finger and thumb Bb key), so your fingering for Eb on most bassoons should be:
(with or without the low Eb key as discussed above)
Don't leave out the fingers in the right hand! If that fingering is too bright/sharp/open sounding some older bassoons prefer the first finger on the right hand instead of the second
But I find that rather uncommon.
M.M.A., D.M.A. University of Illinois at Urbana/Champaign: B.Mus. Lawrence University
Bassoon professor at University of Wisconsin Eau-Claire
Maker of the Little-Jake electric bassoon pickup and Weasel bassoon reeds