A paper wallet is a way of storing private keys which give you control over an Ethereum account (which includes the ether associated with it and any tokens it has). Each account essentially includes a number associated with it (the ether balance) and every ERC20 smart token contract contains a mapping of addresses to token balance. The account balance can't normally be decreased without the private keys and, similarly, the token balance. You will need to store some ether in the associated account to interact with the Augur contract, anyway (such as to send tokens). Thus, not only would they both be accessible afterwards, you pretty much must have ether in the account (unless you plan to never use the Augur tokens).
I'm not really sure why you think you shouldn't have Augur and ETH in the same wallet aside from a worry of putting all your eggs in one basket. In that case, you can keep a bulk of your ether in one account and put the remainder in another paper wallet. But now you have to protect two wallets.