Hello everyone,
Whenever I am traveling with the PMDG Boeing 737-900 (flight plan from Simbrief), I get a warning from ATC shortly after take-off that I should please reset my transponder and set a transponder code (squawk). I would like to do that now. - But the problem is:
I’m always flying in VR, of course I’m always looking forward and my concentration is on the instruments, the yoke and the quadrant (thrust, flaps, etc.) - how am I supposed to be able to set the transponder when it’s quite far back in the middle? I don’t have a co-pilot who could do that for me 
In VR, the fact that I can’t use my hands / fingers makes things even more difficult. Anyone who has ever flown in VR knows that you can only point to the buttons / dials with the controllers and then press / turn them… And that’s just an absolute cramp, there’s no precision whatsoever. That’s really the only thing in VR that’s absolutely no fun.
So how exactly do I solve this now? - How can I set the transponder in flight (or preferably beforehand) during VR? - My previous attempts under the circumstances described above have only ever led to crashes.
Do you have any ideas? - Thanks in advance 
If you are departing IFR you should be getting and setting your Squawk Code when you get your clearance.
Once you get it, you should be inputting, you can have it in standby but once you push back and are ready for taxing you should be squawking mode C.
Are you not getting the squaqk code in your takeoff clearance?
… and if skypilotYTS’ advice doesn’t solve the issue and you are still getting a new code (can happen in real life that ATC asks you to squawk a different code) why don’t you just wait until the autopilot is engaged and then take care of the transponder?
Aviate, navigate, communicate 
Some of us VR users don’t bother with controllers and use a mouse or a trackball.
Engage autopilot shortly after takeoff and set the transponder.
You should get a squawk code when you contact ATC first time while at the gate. You don’t need to wait until you are airborne.
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That’s my problem: I don’t get a transponder code from ATC. I always take off directly on the runway and not at the gate. I’m not quite ready for that much realism yet… Is that the problem?
Would this be the right setting? (Apart from the transponder code, which is of course only an example here)
Correct, that is why you’re not getting the code on the ground because you’re not getting a clearance.
So yes, you’d input the code and set it to TA/RA (Traffic Advisories / Resolution Advisories).
Unless I am mistaken, I believe you can still tune to the clearance frequency and request to file an IFR flight plan even if you spawn on the runway with engines running.
If you don’t want to handle this yourself, you can assign ATC comms to the AI copilot and they will do it for you immediately after begining the flight, including setting the transponder frequency.