The channels allow you to use your radio just as you would with analog repeaters but you get many more options in the digital world. The screen shot below is of the Madison repeater and connecting to it for local communications. Channel 9 is the standard for radio only connections. Be aware that if Channel 9 also has any other group available on its slot, you may have to wait for that channel to finish before getting access.
The digital radio can have a large number of potential channels setup for communications. Start with the basics listing your analog and digital repeaters in an order that makes sense to your use. Do not forget to add simplex channels for analog as well as digital usage.