Programming IC other than arduino board

Hi Guys

im going to build my own board now, and im thinking of using arduino IDE as programmer.

My question is, say i choose different atmel IC than 2560 or 328 or any other than arduino manufacture,just to example ATmega324P-B Automotive or ATxmega64D4 , will i still be able to load program into them?? Is the bootloader specific for the chip?

Another question: If i use 3.3v Design for the IC and the entinre board and my pressure sensor output 4.5v, can i still connect it to the pins? or i need a kind of inverter??

Thanks