How much wiill it be to install my 4 channel car cd player to my 2 channel car amp at best buy?

Best Buy will charge you $50 for the HU and $70-$80 for the amp.

It will cost a lot, because Best Buy will soak you for the price of an amp and CD player install kit.(if not the price of the actual install) And the install quality won't be as good as the kind of work a local car audio shop could do. Also If you have four 12" subs and a 1250 watt amp, they will way overpower your CD player. You will pretty much hear a ton of bass, and your treble will be nonexistent and extremely distorted.

I'm gonna save you some money right now,you hook up the deck like standard,does this deck have a channel(s) for a sub?then you use that channel(s) to your amp.Then the amp to the subs and you should only use 2 of your subs, not 4,you are creating a wrong ohm load on the amp and will do damage to it.If your deck has 4 independant speaker outputs, then use these to power your tweeters or other speakers (full range or two-way) this is the proper way to hook up your system.You don't want to go to best buy for this service, they hire uneducated people to install and they make a lot of mistakes.I have re- installed over 50 systems that were done by best buy in the last 3 yrs.