You need don't two separate amps, you can use 1 easily. You can modify the front doors to get 6.5 speakers but I really don't think its worth it, if your planning on getting a subwoofer down the line. If you really want bass but don't have a subwoofer, just use your 6x9's as bass and don't have to worry about cutting.
By the sound of it, you want to get a coaxial speaker (All-in-one) speakers for your car. Coaxial speakers are great for the back but wrong for the front doors. You would want a component set (Separated speaker parts) to replace the front 5.25 speakers and tweeters. The only true pain is replacing that tweeters, it would vary on the size of the tweeter. On my setup I was able to just jam my infinity tweeter (3/4") into that hole, no worries of screws.
I do understand the 5.25 struggle as theres more 6.5 drivers out there and sometimes even cheaper.
With the amp side, you can just replace the stock amp and don't have to run a single new wire, although its not recommended, especially if you love bass. Stock amp power wiring can handle up to 216 watts (14.4 volts X 15 amps).
