Can I run the Array with only two channels plugged in?

Generally, I am looking to use the Array for movies and general music through an AV Receiver driving all channels. Occasionally, I like to run two channel music from the receiver preamp outs through a dedicated 2 channel amp and onto two speakers for more critical listening. With the Array replacing these two speakers, how would this work?

Do I simply disconnect one channel and run it as before or do I need all three channels hooked up?

Short answer to first question, yes.

Regarding hook up, just connect the L/R channels of the speaker to the two channel amp. As long as the stereo playback mode of the receiver allows for 2.1, you're good to go. No need to connect or disconnect anything.