Decoupling capacitor placements and ratings - how to choose?
You have posed  a very complex question here. It would take me 5 pages to answer this question to the  best of my EE knowledge and abilities. So in the space available I can only offer a few guidelines and principles I have learned about the application of bypass capacitors over many years of design experience.

A. You can never have enough of them.

B. There is no practical way to calculate the required value for a given application. (see G below).

C. There is no practical way to quantitatively assess their effectiveness in the final circuit. (I.e. There is no know "Bypassometer" you can connect to the circuit to measure their actual effect.) The best you can hope for is a "works better" - "works worse" comparative analysis.

D. The reason we use bypass capacitors in the first place is different for different circuit applications &amp; the rules are often confused  or interchanged by unknowledgeable applicators. E.g. Bypass caps are used/required for one reason in applying bipolar TTL 7400 logic circuits. They are also used/required for a different reason in applying CMOS 74HCT00 logic circuits. In op-amps circuits they are used for an entirely different reason, and in motor controls  like yours, yet another reason. Not to mention their use in RF circuits.

E. Allow for different configurations and combinations in your first-cut PCBs. That is add in extras, so you have assembly options when you get to the debug phase of the project. Again, lots of trial and error is necessary, but you can't do that very effectively unless you've planned for it.

F. In general, the lower the frequency of the signals and the larger the currents and resultant energy involved, the larger the bypass capacitors. This the use of electrolytics and tantalums in these situations because they have greater energy storage capabilities and higher current ratings than equivalent capacitance ceramics, plastics and similar wimpy type capacitors.

G. It is practically impossible to calculate the "correct" value for a bypass capacitor because there is no "correct answer" to the problem they are being used to solve. It's a fuzzy problem with a fuzzy solution. You'll encounter this scenario often: One solution fixes certain aspects of the  problem, another solutions fixes other aspects of the problem, no single solution seems to solve all aspects.

H. I like this mechanical engineering analogy: Bypass capacitors are like lock washers in mechanical designs. How do you calculate the size or type of lock washer (e.g. internal star, external star, split ring, etc.) required for a given vibration environment? The answer is you can't. You take a  guess,  if it doesn't work you try the alternatives until you hit on one that gives the desired, or close enough to the desired, results.

You are pretty much on the right track with circuit B - a capacitor per IC. However, I would parallel the 100 nF ceramics with a small tantalum (not electrolytic), say 2.2 to 4.7 MFD (16 WVDC, since your supply is 9 volts, 10 WVDC would be cutting it too close for comfort.) Why? That would take another page or two to explain.

You might submit more focused questions about the same application. E.g. your section #2 would make a good single topic question.

Good Luck and keep your options open!