Rupee to be used for paying wages and military welfare, procuring weapons, ammunition and equipment from Pakistani manufacturers. And since Pakistan buys most of it's equipment from China, thus the yen is to be used.
Only for buying weapons from US Rupee to USD conversion is to be used.
Yen is Japanese currency, Chinese would be Yuan Renmibi.
1 CNY= 16.5 PKR, and 1USD = 6.2 CNY. So whether Pakistan pays in USD or CNY its the same thing.