alpine system from my current car

The Alpine 6.5" (coaxials, I assume) will fit fine in both front & rear factory door locations; but you'll probably want to upgrade the factory tweeters (front only in the non-JBL system, rears too in the JBL version) as well. This is usually accomplished with a set of component speakers, but it's possible to just add a tweeter to your coaxials (using an aftermarket tweet with a capacitor).

The subwoofer can be integrated as well, but you'll probably want to build a new Prius-specific enclosure...there's several good posts here on PriusChat discussing that topic (see eagle33199's posting from 3/24/06).

Adding the amp is also possible; however, if you want to maintain the use of the steering wheel controls and integration of the stereo with the multi-function display, you'll probably want to keep the factory head unit (your Alpine can't do all that....I know, I've got a nice Kenwood Excelon head unit collecting dust!)
To do that, you'll need a line output converter (also several good posts on that topic).

Good luck.....BTW, you'll definately want to upgrade the Factory system based on what you're used to listening to!