I have a 1996 JVC 5 disc changer that I got for free that only has left and right outputs on the back (also compu links but as I understand that is just to outsource the display menus) and I want to connect this to my B&K AVR 307.

which cable should I use and where should I connect to on the receiver?

Also I have a 65in Hitachi HDTV rear projection tv that I would like to connect to my infinity beta 50 speakers I just bought. http://dl.owneriq.net/8/8e9c0a96-6c8...faa779549f.pdf
^^^^a link to the owners manual pg. 9 has the rear panel displayed.
should I use the built in speakers as a center channel or just use my two speakers without a center? I feel like the TV speaker quality is inferior to the quality of my beta 50s

Just use some RCA cables to connect the changer to your receiver, or if you want, you can use either a Toslink or digital coaxial cable to connect it to the receiver. It will be up to you to decide if there is any SQ difference.

I wouldn't use the TV's speakers as a CC. Just select a phantom CC mode in the AVR's speaker set-up menu.