Unless you have a multichannel head unit (DVD, SACD, etc.) the front and rear channels should carry the same signal. Left and right are different (stereo).
You have a 3 RCA outputs (front, rear, sub)? And you have a 4-channel amp and a sub amp. So, why not run front and rear RCAs to the 4-channel, and the 3rd RCA set (I assume is sub preout) to the sub amp?
You can use the y-adapters, but you will lose fading ability (which, IMO, is important in setting up a proper soundstage - Of course, you could simply adjust front/rear gains to do the same thing, just more hassle.), and you will cut down on the quality (voltage) of the input your amp will see.
Question... are you bridging the 4-channel amp to 2-channels to run a single pair of speakers? If this is the case, then the y-adapters may be a better option. Split the front-right channel up and plug into front right and left (for right speaker) and split the front-left channel up and plug into rear right and left (for left speaker).