best way to wire a home theater with tv and dvr

If you'll only watch service-based content, such as Cox programming, Netflix, Vudu, etc...the best soundtracks you'll get would be lossy DD5.1.  Does your TV support outputting DD5.1 signals an A/V receiver?  If so, connect it however you want.  If not, connect your DVR to your A/V receiver.

You didn't mention the make and model of your A/V receiver...so there's chance its video processing would be better than your TV.  Evaluate the video from DVR-to-TV...then DVR-to-A/V receiver-to-TV.

Continuing with the A/V receiver being the central hub for all your source components...will you purchase a Blu-ray player in the future?  If so, start connecting everything through your A/V receiver now.  Blu-ray discs are encoded with high-resolution soundtracks (Dolby TrueHD, DTS-HD) and only an A/V receiver would properly decode and steer those multichannel tracks to the correct speakers.

If you're happy with service-based content going straight to the TV with the option of listening to either the TV speakers or home theater set-up...again...whichever connections you prefer.

Good advice above. Need more info on what your needs are and what your hardware is capable of. Could you list the model numbers of your TV, home theater receiver, any other equipment.