So you can mine multiple pools.
The answer to your original question about mining Litecoin + Novacoin is no, unfortunately. While you
can mine at multiple pools by balancing your submitted shares between them (assuming the pools are all for the same coin, i.e. Litecoin), you will not be mining at
full speed at both of the pools as you're essentially splitting your hashing power between them. The ability to specify more than one pool in cgminer is primarily for failover situations (as Bakemono described) where your miner will automatically submit shares to a backup pool if your preferred pool goes offline for whatever reason. Mining two different coins
simultaneously, as in your Litecoin + Novacoin example is what would be known as merged mining and is currently not possible for any of the scrypt-based coins (Litecoin, Novacoin, Feathercoin, Worldcoin, etc). Where merged mining is possible, i.e. Bitcoin + Namecoin, it's implemented on the pool side and does not require special configuration of cgminer.