I wouldn't choose to play this way, but to try and interpret that formation into FM-speak:
GK - Defend - Neuer
D_C - Defend - Alaba
BPD - Cover - Boateng
D_C - Defend - Benatia
WB_L - Attack - Bernat
DLP - Support - Alonso
RG - Support - Lahm (or Alonso as RG_Support and Lahm as BWM_Support)
WB_R - Attack - Rafinha
AP - Attack - Robben (in the MC position)
AM - Support - Gotze (in the MC position)
F-9 - Support - Lewandowski
Have Neuer Distribute to Defenders and the team play short-passing, possession football and exploit the flanks. The presence of a Regista will help you to maintain possession high up the field and thereby reduce the gap between Robben/Gotze and Lewandowski. By encouraging Alonso to play More Direct Passes you'll get the benefit of his accuracy over distance and ability to switch the play quickly and effectively.
Robben will run at the opposition from deep positions and both Gotze and Lewandowski should be instructed to make runs into the channels. The extent of Lewandowski's isolation up-front will depend on how often you can get Robben onto the ball. Encouraging the team to Run At Opponents (or whatever the actual wording of that Team Instruction is) will often close that gap for you.
I thought Alaba was a wide man rather than a central defender, but perhaps Pep Guardiola has redeployed him into a new role. I don't know if Boateng is really a suitable Ball-Playing Defender but that's the role I prefer to have in the centre of my back-three.
If you try this then I would also experiment with putting the two wing-backs into the MC line, as Wide Midfielders_Support. I played a 3-5-2 system for a while that had a flat midfield 5 and the WMs took good care of the flanks in both attacking and defending situations; the weakness was in the DM position but that shouldn't be a problem for you with Alonso and Lahm on patrol.
