Programming differences between ATTiny stand-alone and programmed via Arduino

Other Hardware 3rd Party Boards
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I just got some ATTiny85's and I'm very excited to start working with them. I also bought the MAKE book on AVR programming.

What I'm a little confused about is the difference between straight C(++) programming of these chips vs programming via Arduino. When you upload a sketch via the Arduino IDE (I'm using the Sparkfun ISP) does it automatically upload the Arduino bootloader, libraries, and everything else I need to run Arduino code? I guess I know that it does, since my test project is working, but I don't understand what the difference would have been had I simply used avrdude and uploaded "classic" C++ code...

Also, what is PORTB? I see a lot of references to that in test code in this book (without much explanation). And it also says that Arduino "ties up" two pins for an internal clock / timer? Does that mean that if you use the Arduino IDE to upload code to an ATMega chip, two pins will automatically be used for some other purpose?

Any other general tips on using ATTiny chips in stand-alone projects while using the Arduino IDE / code?

Thanks!

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osmosis311:
I don't understand what the difference would have been had I simply used avrdude and uploaded "classic" C++ code...

There's no difference.

osmosis311:
Also, what is PORTB?

It's a way of accession the I/O pins dircetly without using digitalWrite();

osmosis311:
Does that mean that if you use the Arduino IDE to upload code to an ATMega chip, two pins will automatically be used for some other purpose?

No.

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Thanks!