If I use diminished chords such as ii diminished chord from the minor scale then do I according to the rules for proper part writing use the first inversion of ii diminished. What is the reasoning behind that? Is it because there is no diminished fifth between the bass and any of the upper voices? But there is a diminished fifth between the the fifth and the root. How come the diminished fifth between the fifth and the root is ignored?
In common-practice part-writing, the notes of a diminished fifth are tendency tones. That means that the notes tend to go somewhere specific in the next chord. A rule of part-writing is not to double tendency tones. The reasoning is that doing so means that the doubled notes would have to resolve the same way, thereby creating parallel octaves (or unisons, rarely).
Also, in most chords, we double either the chord root or the bass note. Since the chord root of ii-diminished is a tendency tone, we must double the bass, which cannot be a tendency tone. The only non-tendency-tone in the ii-diminished triad is its third, so the chord will be in first inversion with a doubled bass.
Further, the most likely destination of this chord is the dominant, then likely the tonic for (perhaps) an authentic cadence. The third of ii-diminished, which is scale degree 4, can go to the root of V naturally in this circumstance. The motion from scale degree 2 to 3 could not fulfill this tendency (and, in fact, we do not immediately resolve it because scale degree 3 is not in the V chord). Putting scale degree 6 in the bass would mean that the ii-diminished triad is in second inversion, which is unstylistic.
Keep in mind that you may more often use ii-half-diminished-7 as your pre-dominant chord in minor. Of course, iv also works.
I would be happy to clarify if needed. Two seconds of Googling did not yield a satisfactory definition of tendency tones, else I would link to one.