So I should avoid importing the private keys and simply use a paper wallet then?
That depends on what you are trying to accomplish.
If you enter your private keys onto any device that is connected to the internet, then you immediately lost the benefit of generating the private keys on an offline computer.
If you want to track the balance on the paper wallets, there are several wallets that allow you to import the bitcoin addresses as "watch only" addresses. This allows you to keep the private keys offline and still have software that displays the total balance to you.