Just in case WiiMC website ever goes down, here is a quote from Tantric
The channel installer is just a forwarder - that means that WiiMC still runs off of SD or USB. The channel looks on SD/USB for apps/wiimc/boot.dol and launches that.
A self-contained channel (with the DOL inside) would be pointless because WiiMC still requires either SD or USB to work.
So what I'm saying is the updating process is the same regardless of if you have the channel installed.