If you set up a virtuzal machine you set it up for solily that purpose. You can make one for each coin if you like that is the good thing about it. Also you can buy usb stick and encrypt them in linux. Very cheap way to be safe.
Edit: yes you can back them up on USB sticks. I will give you an example
Myetherwallet will let you save your wallet in different ways but what i do is just save the private key and the public key on my offline laptop. Then i save them on the encrypted usb sticks. Then i write the private keys down on paper together with the bookings. You should keep bookings on your investment because it can be a mess real fast!
Can you not just copy the whole wallet of each program to a UBS stick from your computer so then you have 2 copies of the same wallet? Or is the only way to only copy both the private & public keys to a USB stick?