Just because your stereo receiver and home theatre amplifier supports 5.1 channels of discrete audio doesn't actually mean you have to use all five channels. If you have only two speakers in your set-up you can still hook them up to your system and watch movies and listen to music. You just won't be taking advantage of all of the audio quality that these media formats support.
Connect your home theatre receiver to your 5.1 amplifier (if applicable). The majority of home theatre receivers purchased today have the amplifier built-in, so you won't actually need to do any connecting. However, if you have an older model, connect your receiver to your amplifier using the audio cables that came with the amp. One end of the cables goes into the "IN" input on the amp, while the other end will go into the "OUT" outputs on the receiver.
Plug one of your two speakers into the input on the receiver labelled "Front Left." Plug the speaker wire that runs off of the speaker into the speaker wire input on the receiver.
Plug the other of your two speakers into the input on the receiver labelled "Front Right." Plug the speaker wire that runs off of the speaker into the speaker wire input on the receiver.
Select "2 Channel Stereo" audio tracks while watching DVD movies (if applicable). Though your home theatre set-up will work just fine with only two speakers hooked up to your 5.1 set-up, most DVDs are mixed in multichannel surround sound. However, if the DVD has a "2 Channel Stereo" option in the "Setup" menu, it will play a specialised track that is designed to take advantage of setups with only two speakers.