Did I buy the wrong thing?

"After speaking with my brother in law, he thinks I made a mistake to try to hook the subs and amp up to my 2 channel JVC cd-player."

are you going to hook the subs directly to the cd player or are you going to hook the amp up to the cd player and the amp will be pushing the subs??

your cd player should have a sub woofer out put (RCAs) on it. on the amp for the input does it have only RCA inputs or does it have RCAs and normal speaker wire input also? you could hook up the amp using the RCAs with no problem and not worry about hurting anything. and samething applies to the speaker wire input.

No offense to your brother in law, but you need to stick to what you can afford. 

Are you sure you just have a two channel JVC cd player?

You need to wire the CD player to the amp(wether it be by RCAs' or by taping to the rear speaker wires and going to the HIgh input on the amp) then have the amp power the box.  Leave everything else in your car alone.  By using the High inputs in the amp it takes the signal from the speaker wire and not the power, so it should not harm the CD player at all.  Now, if you do have a two channel cd player running four speakers then you will have a problem.  But not with the amp or the box, just with the two channel cd player trying to run four speaker and mostlikely seeing a two ohm load now.  If this is the case I would suggest replacing the deck with a four channel deck with some rcas'.

COuld I just hook up the 2 back 6x9's to the sub and just keep a 2  channel cd player?  If not, what is a good cheap 4 channel cd player.   And do yall know a place with guides for installation? (hiding the wires mainly).  Thanks!