Gengis.... That is a very worthwhile subject to raise, indeed organisational skills should be taught, examined and debriefed in an ideal world.
The student is not really helped, as from day one they seem to acquire the wrong equipment, starting with the 'Pilot Case' which may be useful and easy to access by an airline pilot in flight, but once inside a light aircraft, it is of little use. Far better these days, would be a laptop backpack, with lots of compartments and a place to keep the GPS or IPAD.
Once inside the aircraft, such as the PA28 or C152/C172 there is very little space, during a solo flight, a laptop bag can be secured to the pax seat, or failing that is more accessible to the PAX (or examiner). The next thing is where to stow items, most light aircraft have two pockets for the stowage, but really only big enough for a paperback in either side. The logical use of these are one for the pitot cover, fuel strain, control lock and cardboard oil funnel. The other pocket is suited to a checklist, chart and clipboard, but only if they are A5 size. Clearly these need to be stowed for take off, landing and as part of HASSELL checks, but during flight I have not problem with them on top of the instrument panel, as long as they do do cause loss of lookout or reflection.
This leads to a lot of other equipment to be stowed. While there is opposition to flying coveralls in civil aviation, it really solves the problems of stowage. As follows:
LEFT LEG POCKET: En route supplement, which includes frequencies, interception procedure, morse, airport operating times, etc. Protractor and rule for calculating diversions, not the rule needs to be no longer than 15mm and marked in NM and minutes (say at 95 kts TAS.
RIGHT LEG POCKET: Chart, Airfield Plate, PLOG and small tablet.
LEFT LEG KNEE PAD: Notes for times, tach, hobs, defects, and in the pocket underneath a sick bag. Pen torch in pen pocket.
RIGHT LEG KNEE PAD: Notes for clearances, airfield data, etc, pocket underneath spare paper and alcohol wipes for maps
LEFT ARM PEN POCKET: Three Pens (to include one biro and one OHP permanent pen for marking charts)
LEFT BREST POCKET: ID, Driving Licence, Debit Card, Glasses.
RIGHT BREST POCKET: Gloves and mobile phone.
RIGHT THIGH: Scabbard & Knife (for emergencies and inadvertent inflation of life jacket or raft)
The above would pretty much cover you for everything, but the important thing is to have a system that works for you, and every thing is within reach with your eyes closed, the same could be said with any flight bag you use. From my experience, having noted from the pilots candidate the requirement to carry spare glasses, almost always they are not in reach!
Having stated the ideal, I think it is important for the instructor encourage to student to have the best equipment for the job, this does have to involve purchases from Transair, Polleys or the flying club shop, all the things you need can be found in a good stationers such as Staples or for that matter Wilkinsons at a much lower price. I have to say i never really thought much of the kneepads, chinagraphs and those silver analogue stopwatches, far better is a £8 casio watch/stopwatch which you can either wear or velcro onto a kneepad or clipboard.
Getting back to the original question by Ghengis, I am not really sure the management of inflight equipment will ever be taught, yet I think there is a lot of mileage in raising the subject on renewal, both during flight and debriefing. Inflight asking the student to find his spare glasses, during the HASSELL checks asking the student where the pens are stowed and how many were there at the beginning of the flight.