Unless things have changed in the past couple months, the namecoind cli is how you create transactions, manage your namecoin wallet and manage your .bit name registrations.

You'll also need some small amount of namecoin in your wallet to finalize your name registration.  If you want to mine them using the stratum mining protocol you'll need to find a multi-mining pool that support BTC and NMC over stratum.  Many multi-mining pools only support multi-mining for clients using the 'getwork' mining protocol so pick your pool and/or mining protocol carefully and start mining while namecoind initializes (downloads) the block chain.