Ground island or VCC island under IC
Since you are planning to have the two ICs back to back in the circuit board you cannot use the typical technique of putting the bypass caps under the ICs. Also since the two ICs are gull wing leaded parts the best approach is to place the bypass capacitors for each chip right next to the PWR/GND pins of the IC so that there is direct copper connection from the cap to the IC pads. Then connect each PWR and GND pin with vias down into the internal VCC and GND layers. 

Since the space under the QFP-100s will largely not be useful for routing out signals you can arrange to place most of your PWR and GND vias under the ICs instead of outside the IC pin perimeter. If there are some connections between the MCU and the FPGA you could use some of the space under the ICs to interconnect MCU to FPGA. I would suggest that you complete these connections in the layout before committing to the final FPGA pinning so as to optimize the routing under each IC. In any case strongly resist the temptation to cut up the PWR and GND layers to add interconnection signals in those layers, especially under the two ICs. 

Since your MCU has a ADC it probably also has a pair of separate VCCA and GNDA pins. Carefully plan any analog circuitry so that the bypass and any island that you create for these is outside the periphery of the MCU. Aim for having the bypass caps for these be the same as the others (copper direct from caps to IC pins). You can then place single point GND connections for this analog copper at the IC pin - possibly under the IC just inside the IC pad - into the common GND plane.

As you plan a small layout like this it can be good to also allow flexibility on the size selection of bypass capacitor packages. In some cases it may be useful to select 0402 or 0201 packages because of directly adjacent PWR / GND pins. In other cases where there may be signal pins in between the power pins select a larger SMT capacitor so as to bridge the space between the PWR / GND pins and allow routing of signal traces into the IC chip in between the capacitor pads.