Power Switch for PCB in Proteus 7.7
Create a new ATmega symbol that doesn't use a hidden power/ground. Then make an explicit connection from its power to your switch.
This solution is preferred nowadays. Hidden power is rarely used in schematics anymore, since the era of single-power-domain designs is long in the past.
Hidden power/ground came into use during the SSI TTL days. It made manual gate-swap annotations easier. It went out of favor in the 80s, as progammable logic and VLSI replaced random gate logic in most designs.