You may set up ConEmu as default terminal for cmd.exe, tcc.exe, powershell.exe or any other console application. In fact, you choose from what application you need to run any console application, even from Visual Studio for debugging your console applications.
Just turn on checkbox, point applications from you like to start console tools (for example
explorer.exe|totalcmd.exe|wdexpress.exe) and voila. You may press Win+R type
ipconfig /all and press Enter. You may even start your console application in Visual Studio debugger. New console will starts attached to the new ConEmu tab. You may also doubleclick on some executable in the Explorer window.
You may find more information about the feature in the project wiki: DefaultTerminal.
Also, there is an alternative less preferable way to auto run ConEmu on cmd.exe and tcc.exe startup. Just press "Register ConEmu autorun" in Settings -> ComSpec.