Well truthfully, I would ditch those subs and just run a subwoofer in the trunk like you said along with the front speakers. One of the most popular configurations for car audio enthusiasts (as you will find on this site) is a set of component speakers for the front (so 5.5" - 7" midwoofers (depending on space available), tweeters, and crossovers), and a subwoofer setup in the trunk. Not many people here run rear speakers, and if they do it's usually for what is known as rear fill. This is exactly what it sounds like - sound that's meant for the rear just to "fill" it up so the back doesn't sound empty (this is more appearant if you drive a sedan or a large vehicle as such). There are many reasons for a setup like this. Think of it this way - if you ever go to a concert, do you ever see speakers playing music from behind you? No, all the speakers and all the sound is coming to you from the front, from the stage. By not using rear speakers, you can truly optimize your sound stage and get the most from your speakers.
Now, I'm not going to tell you to ditch everything and build a new system from the ground up. But what I can tell you is that this would be the best way to start building a great sounding setup.
Now then, back to your original question. I'd ditch those small 6.5 subs. If you only want to power your front components and a rear subwoofer, here's what I consider your best options:
1) A 4-channel amp bridged to power your front speakers, and a separate monoblock amp for a subwoofer
2) A 4-channel amp with 2 channels powering the fronts, and the other two bridged to power a subwoofer
3) A 2-channel amp for the front comp's and a monoblock amp for a subwoofer.
Which of these three do you think fit you the best? There are other options, but these three are the most common.