Yes, you can connect both a mouse and a keyboard to your laptop and work solely off of the large display if you like by mirroring both screens, or you can keep the laptop open and have two screens to work from, just make sure to adjust their positionings in relation to eachother properly so you dont try to drag things over and nothing happens.
I've a MacBook Pro and a Thunderbolt Display and, 90% of the time, I operate with an Apple USB extended keyboard and a Bluetooth Magic Trackpad. I operate in clamshell mode during that 90% of the time. So, basically, yes, you have an 'iMac' with that configuration.
Easy to do - nice to have all of those ports available - particularly for a Retina that would otherwise need a plethora of adapters.