There is a website charitynavigator.org that rates and evaluates charities. Invisible Children spend 80.5% on program expenses i.e doing what its supposed to do. I think this is a great website to find out where your money is going.
The Ugandan military work with both the UN and the African Union and while I am aware of incidences of Ugandan soldiers being accused and convicted of rape, both the UN and the African Union would not work with a government organisation who used rape as a 'weapon of war'. Are you sure its the actual Ugandan Military?